WebApollo setup questions

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WebApollo setup questions

Robin A. Ohm
Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: WebApollo setup questions

nathandunn

Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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RE: WebApollo setup questions

Robin A. Ohm
Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: WebApollo setup questions

nathandunn

Could you post the JavaScript console logs and you jbrowse trackList.json?  

Looks like it might be a problem on the front end.   

Thanks,

Nathan

On Nov 8, 2015, at 10:33 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Reply | Threaded
Open this post in threaded view
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RE: WebApollo setup questions

Robin A. Ohm
Hi Nathan,

I hope this is what you meant. This is in FireFox after I signed in to webapollo and clicked around a little:
Could not read chrome manifest 'file:///C:/Program%20Files%20(x86)/Mozilla%20Firefox/chrome.manifest'.
While creating services from category 'profile-after-change', service for entry 'Sapi Speech Synth', contract ID '@mozilla.org/synthsapi;1' does not implement nsIObserver.
Get a connection to permissions.sqlite.
mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create xregexp.js:109:17
bad script XDR magic number <unknown>
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="i" modifiers="accel,alt,shift" browser.xul
Use of getPreventDefault() is deprecated.  Use defaultPrevented instead. kwift.FFJETPACK.min.js:1:0
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined index.html:20:9
1447011964072 Toolkit.Telemetry ERROR TelemetryStorage::loadAbortedSessionPing - error removing ping: PingReadError JS Stack trace: [hidden email]:80:15 < TelemetryStorageImpl.loadPingFile<@TelemetryStorage.jsm:1448:13 Log.jsm:749:0
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined



Here's the trackList.json:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "key" : "Reference sequence"
      },
      {
         "trackType" : "HTMLFeatures",
         "label" : "Augustus",
         "key" : "Augustus",
         "type" : "HTMLFeatures",
         "urlTemplate" : "tracks/Augustus/{refseq}/trackData.json",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList"
      }
   ]
}


Thanks again!
R


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Lbl [[hidden email]]
Sent: Sunday, November 08, 2015 19:47
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Could you post the JavaScript console logs and you jbrowse trackList.json?  

Looks like it might be a problem on the front end.   

Thanks,

Nathan

On Nov 8, 2015, at 10:33 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
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Re: WebApollo setup questions

Colin
Hi there,

This type of message indicates the most likely problem:

>ReferenceError: "require is not defined"

This means that the jbrowse or dojo libraries were not initialized properly for whatever reason. Possibly, the first apollo deploy step that was run did not complete properly.

I would run "apollo clean-all" and then "apollo deploy" which will clear out the jbrowse libraries and reinitialize, which is probably the easiest path to fixing things.



-Colin



On Sun, Nov 8, 2015 at 1:53 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:
Hi Nathan,

I hope this is what you meant. This is in FireFox after I signed in to webapollo and clicked around a little:
Could not read chrome manifest 'file:///C:/Program%20Files%20(x86)/Mozilla%20Firefox/chrome.manifest'.
While creating services from category 'profile-after-change', service for entry 'Sapi Speech Synth', contract ID '@mozilla.org/synthsapi;1' does not implement nsIObserver.
Get a connection to permissions.sqlite.
mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create xregexp.js:109:17
bad script XDR magic number <unknown>
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="i" modifiers="accel,alt,shift" browser.xul
Use of getPreventDefault() is deprecated.  Use defaultPrevented instead. kwift.FFJETPACK.min.js:1:0
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined index.html:20:9
1447011964072 Toolkit.Telemetry ERROR TelemetryStorage::loadAbortedSessionPing - error removing ping: PingReadError JS Stack trace: [hidden email]:80:15 < TelemetryStorageImpl.loadPingFile<@TelemetryStorage.jsm:1448:13 Log.jsm:749:0
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined



Here's the trackList.json:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "key" : "Reference sequence"
      },
      {
         "trackType" : "HTMLFeatures",
         "label" : "Augustus",
         "key" : "Augustus",
         "type" : "HTMLFeatures",
         "urlTemplate" : "tracks/Augustus/{refseq}/trackData.json",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList"
      }
   ]
}


Thanks again!
R


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank">+31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Lbl [[hidden email]]
Sent: Sunday, November 08, 2015 19:47

To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Could you post the JavaScript console logs and you jbrowse trackList.json?  

Looks like it might be a problem on the front end.   

Thanks,

Nathan

On Nov 8, 2015, at 10:33 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank">+31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank">+31 (0) 30 2533016




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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RE: WebApollo setup questions

Robin A. Ohm
I tried, but it didn't seem to help. The same messages show up in the js console. I the 'Net' tab in the console browser I noticed error messages concerning dijit, dojo and dojox. The corresponding directories (e.g. /var/lib/tomcat7/webapps/apollo/jbrowse/src/dojo) are present but indeed empty. So it sounds like you've identified the problem, but the proposed fix hasn't worked yet.
Thanks, Robin

Output of "apollo clean-all":
Buildfile: /root/Apollo_2_0_0/Apollo-2.0.0/build.xml

clean:
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse
     [exec] | Loading Grails 2.4.5
     [exec] | Configuring classpath
     [exec] | Configuring classpath.
     [exec] | Environment set to development
     [exec] | Environment set to development.
     [exec] | Environment set to development..
     [exec] | Environment set to development...
     [exec] | Environment set to development....
     [exec] | Environment set to development.....
     [exec] | Application cleaned.

clean-all:
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/WEB-INF/deploy
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/annotator

BUILD SUCCESSFUL
| Application cleaned.




The output of "apollo deploy":
Buildfile: /root/Apollo_2_0_0/Apollo-2.0.0/build.xml

copy.apollo.plugin.webapp:

setup-jbrowse:

git.clone:
     [exec] Submodule 'src/FileSaver' (git://github.com/dkasenberg/FileSaver.js.git) registered for path 'src/FileSaver'
     [exec] Submodule 'src/dbind' (git://github.com/rbuels/dbind.git) registered for path 'src/dbind'
     [exec] Submodule 'src/dgrid' (git://github.com/SitePen/dgrid.git) registered for path 'src/dgrid'
     [exec] Submodule 'src/dijit' (https://github.com/dojo/dijit.git) registered for path 'src/dijit'
     [exec] Submodule 'src/dojo' (https://github.com/dojo/dojo.git) registered for path 'src/dojo'
     [exec] Submodule 'src/dojox' (https://github.com/dojo/dojox.git) registered for path 'src/dojox'
     [exec] Submodule 'src/jDataView' (git://github.com/rbuels/jDataView.git) registered for path 'src/jDataView'
     [exec] Submodule 'src/json-schema' (git://github.com/kriszyp/json-schema.git) registered for path 'src/json-schema'
     [exec] Submodule 'src/jszlib' (git://github.com/rbuels/jszlib.git) registered for path 'src/jszlib'
     [exec] Submodule 'src/lazyload' (git://github.com/rbuels/lazyload.git) registered for path 'src/lazyload'
     [exec] Submodule 'src/put-selector' (git://github.com/kriszyp/put-selector.git) registered for path 'src/put-selector'
     [exec] Submodule 'src/util' (https://github.com/dojo/util.git) registered for path 'src/util'
     [exec] Submodule 'src/xstyle' (git://github.com/kriszyp/xstyle.git) registered for path 'src/xstyle'
     [exec] Result: 1
     [exec] D src/FileSaver

copy.apollo.plugin.jbrowse:
     [echo] copying plugin to jbrowse git ...
     [copy] Copying 188 files to /root/Apollo_2_0_0/Apollo-2.0.0/jbrowse-download/plugins/WebApollo
     [echo] Will be setting up jbrowse
     [copy] Copying 1282 files to /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse
     [copy] Copied 581 empty directories to 12 empty directories under /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse

install.jbrowse.perl:

copy-resources:

javac:
    [mkdir] Created dir: /root/Apollo_2_0_0/Apollo-2.0.0/target/classes/gwt
    [javac] Compiling 62 source files to /root/Apollo_2_0_0/Apollo-2.0.0/target/classes/gwt
    [javac] Note: /root/Apollo_2_0_0/Apollo-2.0.0/src/gwt/org/bbop/apollo/gwt/client/ReferenceSequenceOracle.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
     [copy] Copying 55 files to /root/Apollo_2_0_0/Apollo-2.0.0/target/classes
     [copy] Copied 19 empty directories to 3 empty directories under /root/Apollo_2_0_0/Apollo-2.0.0/target/classes

gwtc:
     [java] Compiling module org.bbop.apollo.gwt.Annotator
     [java]    Compiling 5 permutations
     [java]       Compiling permutation 0...
     [java]       Compiling permutation 1...
     [java]       Compiling permutation 2...
     [java]       Compiling permutation 3...
     [java]       Compiling permutation 4...
     [java]    Compile of permutations succeeded
     [java]    Compilation succeeded -- 128.153s
     [java] Linking into /root/Apollo_2_0_0/Apollo-2.0.0/web-app/annotator
     [java]    Link succeeded
     [java]    Linking succeeded -- 2.186s

BUILD SUCCESSFUL
| Compiling 10 source files

| Compiling 172 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 213 source files

| Compiling 213 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Done creating WAR target/apollo-2.0.0.war


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Colin [[hidden email]]
Sent: Sunday, November 08, 2015 21:28
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions

Hi there,

This type of message indicates the most likely problem:

>ReferenceError: "require is not defined"

This means that the jbrowse or dojo libraries were not initialized properly for whatever reason. Possibly, the first apollo deploy step that was run did not complete properly.

I would run "apollo clean-all" and then "apollo deploy" which will clear out the jbrowse libraries and reinitialize, which is probably the easiest path to fixing things.



-Colin



On Sun, Nov 8, 2015 at 1:53 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:
Hi Nathan,

I hope this is what you meant. This is in FireFox after I signed in to webapollo and clicked around a little:
Could not read chrome manifest 'file:///C:/Program%20Files%20(x86)/Mozilla%20Firefox/chrome.manifest'.
While creating services from category 'profile-after-change', service for entry 'Sapi Speech Synth', contract ID '@mozilla.org/synthsapi;1' does not implement nsIObserver.
Get a connection to permissions.sqlite.
mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create xregexp.js:109:17
bad script XDR magic number <unknown>
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="i" modifiers="accel,alt,shift" browser.xul
Use of getPreventDefault() is deprecated.  Use defaultPrevented instead. kwift.FFJETPACK.min.js:1:0
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined index.html:20:9
1447011964072 Toolkit.Telemetry ERROR TelemetryStorage::loadAbortedSessionPing - error removing ping: PingReadError JS Stack trace: [hidden email]:80:15 < TelemetryStorageImpl.loadPingFile<@TelemetryStorage.jsm:1448:13 Log.jsm:749:0
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined



Here's the trackList.json:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "key" : "Reference sequence"
      },
      {
         "trackType" : "HTMLFeatures",
         "label" : "Augustus",
         "key" : "Augustus",
         "type" : "HTMLFeatures",
         "urlTemplate" : "tracks/Augustus/{refseq}/trackData.json",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList"
      }
   ]
}


Thanks again!
R


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Lbl [[hidden email]]
Sent: Sunday, November 08, 2015 19:47

To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Could you post the JavaScript console logs and you jbrowse trackList.json?  

Looks like it might be a problem on the front end.   

Thanks,

Nathan

On Nov 8, 2015, at 10:33 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016




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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: WebApollo setup questions

Colin
Thanks for the details!

There definitely was an error during your git.clone but it wasn't providing a good error message. My bets are that it was blocking the git:// protocol for you. I added a change to use https:// instead of git:// when cloning jbrowse, so your code should work now if you re-run `apollo clean-all` and `apollo deploy` again.


Thanks for providing all your steps with detailed error messages and for your patience!

Feel free to let us know if you have any other issues
-Colin


PS If I remember correctly, a similar thing had been reported to us by the USDA-NAL but we had not diagnosed the issue at that time


On Sun, Nov 8, 2015 at 3:49 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:
I tried, but it didn't seem to help. The same messages show up in the js console. I the 'Net' tab in the console browser I noticed error messages concerning dijit, dojo and dojox. The corresponding directories (e.g. /var/lib/tomcat7/webapps/apollo/jbrowse/src/dojo) are present but indeed empty. So it sounds like you've identified the problem, but the proposed fix hasn't worked yet.
Thanks, Robin

Output of "apollo clean-all":
Buildfile: /root/Apollo_2_0_0/Apollo-2.0.0/build.xml

clean:
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse
     [exec] | Loading Grails 2.4.5
     [exec] | Configuring classpath
     [exec] | Configuring classpath.
     [exec] | Environment set to development
     [exec] | Environment set to development.
     [exec] | Environment set to development..
     [exec] | Environment set to development...
     [exec] | Environment set to development....
     [exec] | Environment set to development.....
     [exec] | Application cleaned.

clean-all:
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/WEB-INF/deploy
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/annotator

BUILD SUCCESSFUL
| Application cleaned.




The output of "apollo deploy":
Buildfile: /root/Apollo_2_0_0/Apollo-2.0.0/build.xml

copy.apollo.plugin.webapp:

setup-jbrowse:

git.clone:
     [exec] Submodule 'src/FileSaver' (git://github.com/dkasenberg/FileSaver.js.git) registered for path 'src/FileSaver'
     [exec] Submodule 'src/dbind' (git://github.com/rbuels/dbind.git) registered for path 'src/dbind'
     [exec] Submodule 'src/dgrid' (git://github.com/SitePen/dgrid.git) registered for path 'src/dgrid'
     [exec] Submodule 'src/dijit' (https://github.com/dojo/dijit.git) registered for path 'src/dijit'
     [exec] Submodule 'src/dojo' (https://github.com/dojo/dojo.git) registered for path 'src/dojo'
     [exec] Submodule 'src/dojox' (https://github.com/dojo/dojox.git) registered for path 'src/dojox'
     [exec] Submodule 'src/jDataView' (git://github.com/rbuels/jDataView.git) registered for path 'src/jDataView'
     [exec] Submodule 'src/json-schema' (git://github.com/kriszyp/json-schema.git) registered for path 'src/json-schema'
     [exec] Submodule 'src/jszlib' (git://github.com/rbuels/jszlib.git) registered for path 'src/jszlib'
     [exec] Submodule 'src/lazyload' (git://github.com/rbuels/lazyload.git) registered for path 'src/lazyload'
     [exec] Submodule 'src/put-selector' (git://github.com/kriszyp/put-selector.git) registered for path 'src/put-selector'
     [exec] Submodule 'src/util' (https://github.com/dojo/util.git) registered for path 'src/util'
     [exec] Submodule 'src/xstyle' (git://github.com/kriszyp/xstyle.git) registered for path 'src/xstyle'
     [exec] Result: 1
     [exec] D src/FileSaver

copy.apollo.plugin.jbrowse:
     [echo] copying plugin to jbrowse git ...
     [copy] Copying 188 files to /root/Apollo_2_0_0/Apollo-2.0.0/jbrowse-download/plugins/WebApollo
     [echo] Will be setting up jbrowse
     [copy] Copying 1282 files to /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse
     [copy] Copied 581 empty directories to 12 empty directories under /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse

install.jbrowse.perl:

copy-resources:

javac:
    [mkdir] Created dir: /root/Apollo_2_0_0/Apollo-2.0.0/target/classes/gwt
    [javac] Compiling 62 source files to /root/Apollo_2_0_0/Apollo-2.0.0/target/classes/gwt
    [javac] Note: /root/Apollo_2_0_0/Apollo-2.0.0/src/gwt/org/bbop/apollo/gwt/client/ReferenceSequenceOracle.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
     [copy] Copying 55 files to /root/Apollo_2_0_0/Apollo-2.0.0/target/classes
     [copy] Copied 19 empty directories to 3 empty directories under /root/Apollo_2_0_0/Apollo-2.0.0/target/classes

gwtc:
     [java] Compiling module org.bbop.apollo.gwt.Annotator
     [java]    Compiling 5 permutations
     [java]       Compiling permutation 0...
     [java]       Compiling permutation 1...
     [java]       Compiling permutation 2...
     [java]       Compiling permutation 3...
     [java]       Compiling permutation 4...
     [java]    Compile of permutations succeeded
     [java]    Compilation succeeded -- 128.153s
     [java] Linking into /root/Apollo_2_0_0/Apollo-2.0.0/web-app/annotator
     [java]    Link succeeded
     [java]    Linking succeeded -- 2.186s

BUILD SUCCESSFUL
| Compiling 10 source files

| Compiling 172 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 213 source files

| Compiling 213 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Done creating WAR target/apollo-2.0.0.war


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank">+31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Colin [[hidden email]]
Sent: Sunday, November 08, 2015 21:28

To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions

Hi there,

This type of message indicates the most likely problem:

>ReferenceError: "require is not defined"

This means that the jbrowse or dojo libraries were not initialized properly for whatever reason. Possibly, the first apollo deploy step that was run did not complete properly.

I would run "apollo clean-all" and then "apollo deploy" which will clear out the jbrowse libraries and reinitialize, which is probably the easiest path to fixing things.



-Colin



On Sun, Nov 8, 2015 at 1:53 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:
Hi Nathan,

I hope this is what you meant. This is in FireFox after I signed in to webapollo and clicked around a little:
Could not read chrome manifest 'file:///C:/Program%20Files%20(x86)/Mozilla%20Firefox/chrome.manifest'.
While creating services from category 'profile-after-change', service for entry 'Sapi Speech Synth', contract ID '@mozilla.org/synthsapi;1' does not implement nsIObserver.
Get a connection to permissions.sqlite.
mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create xregexp.js:109:17
bad script XDR magic number <unknown>
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="i" modifiers="accel,alt,shift" browser.xul
Use of getPreventDefault() is deprecated.  Use defaultPrevented instead. kwift.FFJETPACK.min.js:1:0
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined index.html:20:9
1447011964072 Toolkit.Telemetry ERROR TelemetryStorage::loadAbortedSessionPing - error removing ping: PingReadError JS Stack trace: [hidden email]:80:15 < TelemetryStorageImpl.loadPingFile<@TelemetryStorage.jsm:1448:13 Log.jsm:749:0
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined



Here's the trackList.json:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "key" : "Reference sequence"
      },
      {
         "trackType" : "HTMLFeatures",
         "label" : "Augustus",
         "key" : "Augustus",
         "type" : "HTMLFeatures",
         "urlTemplate" : "tracks/Augustus/{refseq}/trackData.json",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList"
      }
   ]
}


Thanks again!
R


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Lbl [[hidden email]]
Sent: Sunday, November 08, 2015 19:47

To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Could you post the JavaScript console logs and you jbrowse trackList.json?  

Looks like it might be a problem on the front end.   

Thanks,

Nathan

On Nov 8, 2015, at 10:33 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank"> +31 (0) 30 2533016




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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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RE: WebApollo setup questions

Robin A. Ohm
Hi Colin and Nathan,

Yes, this time it worked perfectly. Thank you both for your excellent help!

Best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Colin [[hidden email]]
Sent: Sunday, November 08, 2015 23:27
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions

Thanks for the details!

There definitely was an error during your git.clone but it wasn't providing a good error message. My bets are that it was blocking the git:// protocol for you. I added a change to use https:// instead of git:// when cloning jbrowse, so your code should work now if you re-run `apollo clean-all` and `apollo deploy` again.


Thanks for providing all your steps with detailed error messages and for your patience!

Feel free to let us know if you have any other issues
-Colin


PS If I remember correctly, a similar thing had been reported to us by the USDA-NAL but we had not diagnosed the issue at that time


On Sun, Nov 8, 2015 at 3:49 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:
I tried, but it didn't seem to help. The same messages show up in the js console. I the 'Net' tab in the console browser I noticed error messages concerning dijit, dojo and dojox. The corresponding directories (e.g. /var/lib/tomcat7/webapps/apollo/jbrowse/src/dojo) are present but indeed empty. So it sounds like you've identified the problem, but the proposed fix hasn't worked yet.
Thanks, Robin

Output of "apollo clean-all":
Buildfile: /root/Apollo_2_0_0/Apollo-2.0.0/build.xml

clean:
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse
     [exec] | Loading Grails 2.4.5
     [exec] | Configuring classpath
     [exec] | Configuring classpath.
     [exec] | Environment set to development
     [exec] | Environment set to development.
     [exec] | Environment set to development..
     [exec] | Environment set to development...
     [exec] | Environment set to development....
     [exec] | Environment set to development.....
     [exec] | Application cleaned.

clean-all:
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/WEB-INF/deploy
   [delete] Deleting directory /root/Apollo_2_0_0/Apollo-2.0.0/web-app/annotator

BUILD SUCCESSFUL
| Application cleaned.




The output of "apollo deploy":
Buildfile: /root/Apollo_2_0_0/Apollo-2.0.0/build.xml

copy.apollo.plugin.webapp:

setup-jbrowse:

git.clone:
     [exec] Submodule 'src/FileSaver' (git://github.com/dkasenberg/FileSaver.js.git) registered for path 'src/FileSaver'
     [exec] Submodule 'src/dbind' (git://github.com/rbuels/dbind.git) registered for path 'src/dbind'
     [exec] Submodule 'src/dgrid' (git://github.com/SitePen/dgrid.git) registered for path 'src/dgrid'
     [exec] Submodule 'src/dijit' (https://github.com/dojo/dijit.git) registered for path 'src/dijit'
     [exec] Submodule 'src/dojo' (https://github.com/dojo/dojo.git) registered for path 'src/dojo'
     [exec] Submodule 'src/dojox' (https://github.com/dojo/dojox.git) registered for path 'src/dojox'
     [exec] Submodule 'src/jDataView' (git://github.com/rbuels/jDataView.git) registered for path 'src/jDataView'
     [exec] Submodule 'src/json-schema' (git://github.com/kriszyp/json-schema.git) registered for path 'src/json-schema'
     [exec] Submodule 'src/jszlib' (git://github.com/rbuels/jszlib.git) registered for path 'src/jszlib'
     [exec] Submodule 'src/lazyload' (git://github.com/rbuels/lazyload.git) registered for path 'src/lazyload'
     [exec] Submodule 'src/put-selector' (git://github.com/kriszyp/put-selector.git) registered for path 'src/put-selector'
     [exec] Submodule 'src/util' (https://github.com/dojo/util.git) registered for path 'src/util'
     [exec] Submodule 'src/xstyle' (git://github.com/kriszyp/xstyle.git) registered for path 'src/xstyle'
     [exec] Result: 1
     [exec] D src/FileSaver

copy.apollo.plugin.jbrowse:
     [echo] copying plugin to jbrowse git ...
     [copy] Copying 188 files to /root/Apollo_2_0_0/Apollo-2.0.0/jbrowse-download/plugins/WebApollo
     [echo] Will be setting up jbrowse
     [copy] Copying 1282 files to /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse
     [copy] Copied 581 empty directories to 12 empty directories under /root/Apollo_2_0_0/Apollo-2.0.0/web-app/jbrowse

install.jbrowse.perl:

copy-resources:

javac:
    [mkdir] Created dir: /root/Apollo_2_0_0/Apollo-2.0.0/target/classes/gwt
    [javac] Compiling 62 source files to /root/Apollo_2_0_0/Apollo-2.0.0/target/classes/gwt
    [javac] Note: /root/Apollo_2_0_0/Apollo-2.0.0/src/gwt/org/bbop/apollo/gwt/client/ReferenceSequenceOracle.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
     [copy] Copying 55 files to /root/Apollo_2_0_0/Apollo-2.0.0/target/classes
     [copy] Copied 19 empty directories to 3 empty directories under /root/Apollo_2_0_0/Apollo-2.0.0/target/classes

gwtc:
     [java] Compiling module org.bbop.apollo.gwt.Annotator
     [java]    Compiling 5 permutations
     [java]       Compiling permutation 0...
     [java]       Compiling permutation 1...
     [java]       Compiling permutation 2...
     [java]       Compiling permutation 3...
     [java]       Compiling permutation 4...
     [java]    Compile of permutations succeeded
     [java]    Compilation succeeded -- 128.153s
     [java] Linking into /root/Apollo_2_0_0/Apollo-2.0.0/web-app/annotator
     [java]    Link succeeded
     [java]    Linking succeeded -- 2.186s

BUILD SUCCESSFUL
| Compiling 10 source files

| Compiling 172 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 213 source files

| Compiling 213 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Done creating WAR target/apollo-2.0.0.war


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Colin [[hidden email]]
Sent: Sunday, November 08, 2015 21:28

To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions

Hi there,

This type of message indicates the most likely problem:

>ReferenceError: "require is not defined"

This means that the jbrowse or dojo libraries were not initialized properly for whatever reason. Possibly, the first apollo deploy step that was run did not complete properly.

I would run "apollo clean-all" and then "apollo deploy" which will clear out the jbrowse libraries and reinitialize, which is probably the easiest path to fixing things.



-Colin



On Sun, Nov 8, 2015 at 1:53 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:
Hi Nathan,

I hope this is what you meant. This is in FireFox after I signed in to webapollo and clicked around a little:
Could not read chrome manifest 'file:///C:/Program%20Files%20(x86)/Mozilla%20Firefox/chrome.manifest'.
While creating services from category 'profile-after-change', service for entry 'Sapi Speech Synth', contract ID '@mozilla.org/synthsapi;1' does not implement nsIObserver.
Get a connection to permissions.sqlite.
mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial [[Prototype]] value using Object.create xregexp.js:109:17
bad script XDR magic number <unknown>
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="i" modifiers="accel,alt,shift" browser.xul
Use of getPreventDefault() is deprecated.  Use defaultPrevented instead. kwift.FFJETPACK.min.js:1:0
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
TypeError: KWKwiftDebugger.loadStarts is not a function core.js:585:1
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined index.html:20:9
1447011964072 Toolkit.Telemetry ERROR TelemetryStorage::loadAbortedSessionPing - error removing ping: PingReadError JS Stack trace: [hidden email]:80:15 < TelemetryStorageImpl.loadPingFile<@TelemetryStorage.jsm:1448:13 Log.jsm:749:0
ReferenceError: require is not defined init.js:1:1
ReferenceError: require is not defined



Here's the trackList.json:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "key" : "Reference sequence"
      },
      {
         "trackType" : "HTMLFeatures",
         "label" : "Augustus",
         "key" : "Augustus",
         "type" : "HTMLFeatures",
         "urlTemplate" : "tracks/Augustus/{refseq}/trackData.json",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList"
      }
   ]
}


Thanks again!
R


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Lbl [[hidden email]]
Sent: Sunday, November 08, 2015 19:47

To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Could you post the JavaScript console logs and you jbrowse trackList.json?  

Looks like it might be a problem on the front end.   

Thanks,

Nathan

On Nov 8, 2015, at 10:33 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for your quick reply. I hadn't realized that those were release candidates. I followed the installation instructions in the readthedocs, so I used git to get the code.
I've tried again with version 2.0.0. I'm not trying to migrate a database, so I dropped and recreated the mysql tables. I deployed by running './apollo deploy'. Stopped tomcat7, removed the other apollo instances, copied to new war file into the webapps dir, restarted tomcat7. After a few mins the database schema is installed, so it looks like database access is ok. I open a private window in Chrome and go to the url. Looks fine, I register an admin. I create an organism using a data directory that works well in a jbrowse instance on the same server. In WebApollo the jbrowse panel doesn't load, though. Also, the "Tracks" tab doesn't list any tracks. I could create new users and assign permissions.

Below this email I've pasted the part of catalina.out that is added during a tomcat7 restart. It has several warnings and errors, but I'm not sure what they mean. Unfortunately my knowledge of tomcat/cataline/java is very limited.

Thanks again for your help! Best regards,

Robin


Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@59772fe8]) and a value of type [com.codahale.metrics.ThreadLocalRand
om] (value [com.codahale.metrics.ThreadLocalRandom@1fea563b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.Conver
tersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@6fae63ff]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:20 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:22 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Nov 08, 2015 7:11:24 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2165 ms
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 08, 2015 7:11:24 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Nov 08, 2015 7:11:24 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 08, 2015 7:11:57 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
Nov 08, 2015 7:13:38 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Nov 08, 2015 7:13:39 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 08, 2015 7:13:39 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 134628 ms

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Sunday, November 08, 2015 17:45
To: [hidden email]
Subject: Re: [apollo] WebApollo setup questions


Those don’t sound correct.   It sounds like you’re pulling off of master (RC5-SNAPSHOT stands for release candidate 5 snapshot), which might be sort of hit and miss, though we haven’t run into this exact problem yet and it HAS been pretty stable (we use it daily).

So my guess is that:

1 - the browser cache is still using some of the older code 
2 - the database is having issues migrating your schema

My suggestion if you want to live on the edge (pulling from master):
A - always backup your data before doing an update (in H2 just make a copy, postgresql, mysql should have their own tools for this).  We handle schema changes between 2.0.0 and 2.0.1 (which is not live yet), but not necessarily in-between
B - refresh your screen pressing shift while reloading (this should empty the cache . . .at least on chrome) . . or try a private / incognito window .  .. this should address the caching problem
C - post your tomcat log (catalina.out) . . often there is a small schema error that the code isn’t handling properly which can be fixed with a few SQL commands.
D - and let us know what you’re using for a backing data store and how much prior data you have . .  using a de novo database should always work, but not if you have annotations to save (C is usually pretty easy, as well).

To play it safe, you could still use 2.0.0 and then upgrade to 2.0.1 when that is released (hopefully soon .  . hopefully in November). 

Let us know how this goes. 

Nathan

On Nov 8, 2015, at 4:22 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hello,

I'm trying to set up WebApollo, but I've run into some problems.

- I tried version 2.0.1-RC5-SNAPSHOT. After creating a new organism the Jbrowse panel doesn't load correctly. It just stays white. I also can't change user permissions: they aren't saved.
- Next, I tried an older version (2.0.1-SNAPSHOT, downloaded on 12 Aug 2015) which has previously worked fine for me on another server. This time the problems I mention above didn't happen. However, when I drag a gene into the "User-created Annotations" track it initially doesn't show up. When I hit refresh on the browser it does show up. Also, the "Annotations" tab keeps showing "No results", even though several annotations in fact exist. These problems didn't happen when I tried this version of WebApollo on another server.

My guess is that some of the settings of tomcat7/catalina/java are incorrect, but I don't know how to fix this, or even how to troubleshoot it. I tried the suggested CATALINA_OPTS that are mentioned in the Troubleshooting Guide, but this didn't help.

Do these issues sound familiar and/or does anyone know how to fix it? Any help would be greatly appreciated.

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="&#43;31302533016" target="_blank"> +31 (0) 30 2533016




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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