Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

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Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Henry
Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry




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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

nathandunn

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Henry
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

nathandunn

When it installs JBrowse in 2.0.2 it does a recursive clone of jbrowse to install it (this will be fixed in 2.0.3), which sometimes stalls.  

I would suggest doing an “./apollo clean-all” and then an “./apollo deploy”, but tracking the build output in case it fails again you can send out the build information.  

If that doesn’t work, we can meet briefly and sort it out.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On May 4, 2016, at 2:00 PM, Nathan Henry <[hidden email]> wrote:

Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Loraine Guéguen-2
In reply to this post by Henry
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Loraine Guéguen-2
Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





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: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

nathandunn

JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse.   Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3).     I would recommend the 2.0.2 version.

To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”).   Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way.   After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).
 
I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).  

Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On May 23, 2016, at 6:56 AM, Loraine Guéguen <[hidden email]> wrote:

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Henry
Hi Loraine,

./apollo clean-all and then ./apollo deploy did not work for me.

Unfortunately, I have not had time to troubleshoot this further.

However, I am sure Nathan and the Apollo team will be able to help sort this out.

Henry

On Mon, May 23, 2016 at 11:43 AM, Nathan Dunn <[hidden email]> wrote:

JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse.   Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3).     I would recommend the 2.0.2 version.

To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”).   Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way.   After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).
 
I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).  

Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On May 23, 2016, at 6:56 AM, Loraine Guéguen <[hidden email]> wrote:

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

nathandunn
In reply to this post by Loraine Guéguen-2

Loraine,

I think that Nathan (the other one) stuck with 2.0.0.  

However, if there are ways we could improve the build in 2.0.3, the Apollo team would definitely like to know.  

Nathan

On May 23, 2016, at 6:56 AM, Loraine Guéguen <[hidden email]> wrote:

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Loraine Guéguen-2
In reply to this post by nathandunn
Hi Nathan,

To let you know what we did :
We finally installed version 2.0.2 with git, but because we were not able to get the JBrowse with clean-all, rm and deploy (empty jbrowse-download directory), we copied the content of the jbrowse-download directory obtained from the apollo tar.gz archive.

Maybe this issue is solved in the 2.0.3.
Thanks

Loraine Guéguen


Le 23/05/2016 17:43, Nathan Dunn a écrit :

JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse.   Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3).     I would recommend the 2.0.2 version.

To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”).   Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way.   After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).
 
I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).  

Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On May 23, 2016, at 6:56 AM, Loraine Guéguen <[hidden email]> wrote:

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

nathandunn

It should be significantly better with the 2.0.3 release (which is released):  https://github.com/GMOD/Apollo/tree/2.0.3

The only caveat is you need to install node.js and bower (npm install -g bower), but I haven’t run into any further git clone issues with JBrowse since. 

Please let me know if you run into any issues.  

Nathan

On Jun 28, 2016, at 11:29 AM, Loraine Guéguen <[hidden email]> wrote:

Hi Nathan,

To let you know what we did :
We finally installed version 2.0.2 with git, but because we were not able to get the JBrowse with clean-all, rm and deploy (empty jbrowse-download directory), we copied the content of the jbrowse-download directory obtained from the apollo tar.gz archive.

Maybe this issue is solved in the 2.0.3.
Thanks

Loraine Guéguen


Le 23/05/2016 17:43, Nathan Dunn a écrit :

JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse.   Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3).     I would recommend the 2.0.2 version.

To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”).   Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way.   After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).
 
I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).  

Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On May 23, 2016, at 6:56 AM, Loraine Guéguen <[hidden email]> wrote:

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email][hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email][hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

Henry
Hi Loraine,

Thanks for lettings us know!

Henry

On Tue, Jun 28, 2016 at 11:44 AM, Nathan Dunn <[hidden email]> wrote:

It should be significantly better with the 2.0.3 release (which is released):  https://github.com/GMOD/Apollo/tree/2.0.3

The only caveat is you need to install node.js and bower (npm install -g bower), but I haven’t run into any further git clone issues with JBrowse since. 

Please let me know if you run into any issues.  

Nathan

On Jun 28, 2016, at 11:29 AM, Loraine Guéguen <[hidden email]> wrote:

Hi Nathan,

To let you know what we did :
We finally installed version 2.0.2 with git, but because we were not able to get the JBrowse with clean-all, rm and deploy (empty jbrowse-download directory), we copied the content of the jbrowse-download directory obtained from the apollo tar.gz archive.

Maybe this issue is solved in the 2.0.3.
Thanks

Loraine Guéguen


Le 23/05/2016 17:43, Nathan Dunn a écrit :

JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse.   Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3).     I would recommend the 2.0.2 version.

To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”).   Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way.   After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).
 
I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).  

Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On May 23, 2016, at 6:56 AM, Loraine Guéguen <[hidden email]> wrote:

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen
 

Le 23/05/2016 15:26, Loraine Guéguen a écrit :
Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Le 04/05/2016 23:00, Nathan Henry a écrit :
Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.

Do  you have other suggestions?

Thank you for your time,

Henry


On Wed, May 4, 2016 at 4:40 PM, Nathan Dunn <[hidden email][hidden email]> wrote:

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases)?  If its the former you’ll want to do a “./apollo clean-all” before you rebuild.  

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory.   e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory.   You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.   

Nathan

On May 4, 2016, at 1:29 PM, Nathan Henry <[hidden email][hidden email]> wrote:

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.

My console error is as follows:

ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],


The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.

I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry



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][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. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




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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