Re: GMOD project

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Re: GMOD project

Scott Cain
Hi Luciano,

I cc'ed the apollo mailing list--they might be able to help with getting Apollo installed.

Unfortunately, the GMOD in the Cloud server is the same age as the VirtualBox instance.  What are you interested in doing? Do you only want Apollo and JBrowse, or do you have something else in mind?  What kind of data do you have?

Scott



On Mon, Jan 6, 2020 at 9:08 AM Luciano Kalabric Silva <[hidden email]> wrote:

Hi Scott,

 

Good to know. I read you have an instance in the Cloud at AWS. I created an account there. How do I do to access GMOD in the Cloud? Is it free?

Since the VBox is not up-to-date, I do not know if my colleagues will allow me to make it available in our network (security issues).

 

I am trying to install Apollo and Jbrowse from scratch on Ubuntu Server 19.01 (64bits). I could do JBrowse and it seems to be working fine but Apollo is still giving me some problems! When I tried to deploy, it tried to check/install JBrowse again, if I am not mistaken. There are a couple of warnings I will try to figure out.

 

If possible, I would like to test GMOD. How do I do today?

 

Thanks for your prompt answer,

 

Luciano Kalabric.

 

 

 

De: Scott Cain <[hidden email]>
Enviada em: segunda-feira, 6 de janeiro de 2020 13:50
Para: Luciano Kalabric Silva <[hidden email]>
Cc: [hidden email]
Assunto: Re: GMOD project

 

Hi Luciano,

 

Yes, the GMOD project is still active.  At around 2015, we went from two full time people working specifically on GMOD to a third of a person (me), but many of the core projects are still actively developed (Chado, Tripal, JBrowse, Apollo, Galaxy, and InterMine to name a few).  Unfortunately, I don't really have time to make a new VirtualBox instance, but I have toyed with the idea of recreating much of the same functionality with Docker, since most of the projects have docker files.

 

Please let me know if you have any questions,

Scott

 

 

On Mon, Jan 6, 2020 at 5:04 AM Luciano Kalabric Silva <[hidden email]> wrote:

Hi,

 

First of all, I would like to know if GMOD project is still active. I visited your web site and most things were up-to-date 2014. I am really interested to set up a server in my institution and I downloaded the VBox to test it. Unfortunately, most of the programs are old and I could not update them all! Is there any telephone or chat program we can use to communicate with you guys?

 

Thank,

 

Luciano Kalabric.



--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GMOD project

nathandunn

Luciano, I think we are all still here!

To use Apollo I recommend one of 4 solutions:

1 - Just get an account on the European use galaxy server.  They provide a JBrowse and an Apollo instance:  https://annotation.usegalaxy.eu/. It is free and no install required. 
3 - Load Apollo as an EC2 image from the AWS Marketplace.  We should have the most recent version (2.5.0) on the N. Virginia server)
4 - Install locally (what you are no doubt trying): https://genomearchitect.readthedocs.io/en/latest/Setup.html


If you need to install locally and its not working, please post any issues run into here on this mailing list.  (To sign up for the mailing list go here: https://groups.google.com/a/lbl.gov/forum/#!forum/apollo)

Cheers,

Nathan


On Jan 6, 2020, at 7:40 AM, Scott Cain <[hidden email]> wrote:

Hi Luciano,

I cc'ed the apollo mailing list--they might be able to help with getting Apollo installed.

Unfortunately, the GMOD in the Cloud server is the same age as the VirtualBox instance.  What are you interested in doing? Do you only want Apollo and JBrowse, or do you have something else in mind?  What kind of data do you have?

Scott



On Mon, Jan 6, 2020 at 9:08 AM Luciano Kalabric Silva <[hidden email]> wrote:

Hi Scott,

 

Good to know. I read you have an instance in the Cloud at AWS. I created an account there. How do I do to access GMOD in the Cloud? Is it free?

Since the VBox is not up-to-date, I do not know if my colleagues will allow me to make it available in our network (security issues).

 

I am trying to install Apollo and Jbrowse from scratch on Ubuntu Server 19.01 (64bits). I could do JBrowse and it seems to be working fine but Apollo is still giving me some problems! When I tried to deploy, it tried to check/install JBrowse again, if I am not mistaken. There are a couple of warnings I will try to figure out.

 

If possible, I would like to test GMOD. How do I do today?

 

Thanks for your prompt answer,

 

Luciano Kalabric.

 

 

 

De: Scott Cain <[hidden email]>
Enviada em: segunda-feira, 6 de janeiro de 2020 13:50
Para: Luciano Kalabric Silva <[hidden email]>
Cc: [hidden email]
Assunto: Re: GMOD project

 

Hi Luciano,

 

Yes, the GMOD project is still active.  At around 2015, we went from two full time people working specifically on GMOD to a third of a person (me), but many of the core projects are still actively developed (Chado, Tripal, JBrowse, Apollo, Galaxy, and InterMine to name a few).  Unfortunately, I don't really have time to make a new VirtualBox instance, but I have toyed with the idea of recreating much of the same functionality with Docker, since most of the projects have docker files.

 

Please let me know if you have any questions,

Scott

 

 

On Mon, Jan 6, 2020 at 5:04 AM Luciano Kalabric Silva <[hidden email]> wrote:

Hi,

 

First of all, I would like to know if GMOD project is still active. I visited your web site and most things were up-to-date 2014. I am really interested to set up a server in my institution and I downloaded the VBox to test it. Unfortunately, most of the programs are old and I could not update them all! Is there any telephone or chat program we can use to communicate with you guys?

 

Thank,

 

Luciano Kalabric.



--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GMOD project

nathandunn
In reply to this post by Scott Cain

You can still use docker, but this should work.

I didn’t see a problem with your setup.  What happens when you connect to the server at:

http://server:8080/apollo 

?

Nathan

On Jan 6, 2020, at 5:34 PM, Luciano Kalabric Silva <[hidden email]> wrote:



Hi Dunn,


Thank you! I am really trying to install Apollo in a new Ubuntu Server I have. 


I read all tutorials possible and now I am reviewing things according to https://genomearchitect.readthedocs.io/en/latest/ExampleBuild.html


When I ran ./apollo run-local, that's what I get:

root@ubuntu-server:~/src/Apollo-2.5.0# ./apollo run-local
Using gradlew
Gradle version: 2.11
Node Version: 10
Npm Version: 6
Yarn Version: 1
javac 1.8.0_232 found
javac installed
JDK 1.8 found: javac 1.8.0_232
Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.16.6-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], NeatHTMLFeatures:[included:true, linearGradient:0], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
Final plugins [WebApollo:[included:true], NeatHTMLFeatures:[included:true, linearGradient:0], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
:installJBrowseWebOnly
JBrowse already exists
From https://github.com/gmod/jbrowse
 * tag                 1.16.6-release -> FETCH_HEAD
Already up to date.
yarn install v1.21.1
warning package.json: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning package.json: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
[1/4] Resolving packages...
[2/4] Fetching packages...
info fsevents@1.2.9: The platform "linux" is incompatible with this module.
info "fsevents@1.2.9" is an optional dependency and failed compatibility check. Excluding it from installation.
[3/4] Linking dependencies...
warning " > dojo-webpack-plugin@2.8.9" has unmet peer dependency "webpack-sources@>=1.0.1".
warning " > url-loader@0.5.7" has unmet peer dependency "file-loader@*".
[4/4] Building fresh packages...

Do you know is those warnings interfere in anything? And what about those one in steps [2/4] and [3/4]?


Is there anything I can do?


Thank you,


Luciano Kalabric.



De: Nathan Dunn <[hidden email]>
Enviado: segunda-feira, 6 de janeiro de 2020 16:17:27
Para: Scott Cain
Cc: Luciano Kalabric Silva; [hidden email]
Assunto: Re: [apollo] GMOD project
 

Luciano, I think we are all still here!

To use Apollo I recommend one of 4 solutions:

1 - Just get an account on the European use galaxy server.  They provide a JBrowse and an Apollo instance:  https://annotation.usegalaxy.eu/. It is free and no install required. 
3 - Load Apollo as an EC2 image from the AWS Marketplace.  We should have the most recent version (2.5.0) on the N. Virginia server)
4 - Install locally (what you are no doubt trying): https://genomearchitect.readthedocs.io/en/latest/Setup.html


If you need to install locally and its not working, please post any issues run into here on this mailing list.  (To sign up for the mailing list go here: https://groups.google.com/a/lbl.gov/forum/#!forum/apollo)

Cheers,

Nathan


On Jan 6, 2020, at 7:40 AM, Scott Cain <[hidden email]> wrote:

Hi Luciano,

I cc'ed the apollo mailing list--they might be able to help with getting Apollo installed.

Unfortunately, the GMOD in the Cloud server is the same age as the VirtualBox instance.  What are you interested in doing? Do you only want Apollo and JBrowse, or do you have something else in mind?  What kind of data do you have?

Scott



On Mon, Jan 6, 2020 at 9:08 AM Luciano Kalabric Silva <[hidden email]> wrote:

Hi Scott,

 

Good to know. I read you have an instance in the Cloud at AWS. I created an account there. How do I do to access GMOD in the Cloud? Is it free?

Since the VBox is not up-to-date, I do not know if my colleagues will allow me to make it available in our network (security issues).

 

I am trying to install Apollo and Jbrowse from scratch on Ubuntu Server 19.01 (64bits). I could do JBrowse and it seems to be working fine but Apollo is still giving me some problems! When I tried to deploy, it tried to check/install JBrowse again, if I am not mistaken. There are a couple of warnings I will try to figure out.

 

If possible, I would like to test GMOD. How do I do today?

 

Thanks for your prompt answer,

 

Luciano Kalabric.

 

 

 

De: Scott Cain <[hidden email]>
Enviada em: segunda-feira, 6 de janeiro de 2020 13:50
Para: Luciano Kalabric Silva <[hidden email]>
Cc: [hidden email]
Assunto: Re: GMOD project

 

Hi Luciano,

 

Yes, the GMOD project is still active.  At around 2015, we went from two full time people working specifically on GMOD to a third of a person (me), but many of the core projects are still actively developed (Chado, Tripal, JBrowse, Apollo, Galaxy, and InterMine to name a few).  Unfortunately, I don't really have time to make a new VirtualBox instance, but I have toyed with the idea of recreating much of the same functionality with Docker, since most of the projects have docker files.

 

Please let me know if you have any questions,

Scott

 

 

On Mon, Jan 6, 2020 at 5:04 AM Luciano Kalabric Silva <[hidden email]> wrote:

Hi,

 

First of all, I would like to know if GMOD project is still active. I visited your web site and most things were up-to-date 2014. I am really interested to set up a server in my institution and I downloaded the VBox to test it. Unfortunately, most of the programs are old and I could not update them all! Is there any telephone or chat program we can use to communicate with you guys?

 

Thank,

 

Luciano Kalabric.



--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GMOD project

nathandunn


So, the documentation could be better (feel free to edit), but if you copy one of the sample-apollo-config.groovy files over you add the plugins directly.


You should be able to set the JBrowse plugins you want to activate directly and they will automatically get cloned and added.  For example:


Once  you run ./apollo deploy it will build a war file in the target directory (apollo-2.5.0.war).  This gets copied into web apps directory.


What I would do:

0 - make sure that you either don’t have gradle and grails installed (it will download the right version) or if they are installed the active versions are 2.5.5 for grails and 2.4.7 for gradle (I think that is why you are getting the error below).
1 - start with a fresh download / clone of apollo
2 - copy a sample config to apollo-config.groovy
3 - edit the apollo-config.groovy to add the jbrowse plugins you want
4 - ./apollo deploy 
5 - copy built war file into the tomcat webapps directory as apollo.war (or whatever you want)
6 - start tomcat and connect



Nathan


On Jan 7, 2020, at 5:14 AM, Luciano Kalabric Silva <[hidden email]> wrote:

Hi,

I see my mistake. I removed my jbrowse folder from the web server and copied Apollo-2.5.0 into apollo/ there. Then I stopped tomcap to run ./apollo run-local. In the very end of the process I got this:  

| Error Error initializing classpath: No builders are available to build a model of type 'org.grails.gradle.plugin.model.GrailsClasspath'. (Use --stacktrace to see the full trace)

All dependencies were solved but I still look like a dog chasing its own tail!


Do you guys, passed through the same issue? How do I do to finally install Apollo!

Eventually, I will return to my old and good Artemis and just use jbrowse to share online!

Thanks,

Luciano Kalabric.

 





De: Luciano Kalabric Silva
Enviado: terça-feira, 7 de janeiro de 2020 08:42:52
Para: Lbl
Cc: Scott Cain; [hidden email]
Assunto: Re: [apollo] GMOD project
 
Hi,

Yesterday I figured out that nlm does not solve dependencies, so I installed the remains packages on my own. 

I installed JBrowse first, so I have an URL http://server:8080/jbrowse

I do not have any http://server:8080/apollo yet. I understood that I should ./apollo deploy and copy the jbrowse/plugins/WebApollo generated into http://server:8080/jbrowse/plugins, and activate it by editing jbrowse.conf and re-run ./setup.sh. Isn´t it?

Luciano Kalabric.

De: Lbl <[hidden email]>
Enviado: terça-feira, 7 de janeiro de 2020 02:11:51
Para: Luciano Kalabric Silva
Cc: Scott Cain; [hidden email]
Assunto: Re: [apollo] GMOD project
 

You can still use docker, but this should work.

I didn’t see a problem with your setup.  What happens when you connect to the server at:


?

Nathan

On Jan 6, 2020, at 5:34 PM, Luciano Kalabric Silva <[hidden email]> wrote:


Hi Dunn,

Thank you! I am really trying to install Apollo in a new Ubuntu Server I have. 

I read all tutorials possible and now I am reviewing things according to https://genomearchitect.readthedocs.io/en/latest/ExampleBuild.html

When I ran ./apollo run-local, that's what I get:

root@ubuntu-server:~/src/Apollo-2.5.0# ./apollo run-local
Using gradlew
Gradle version: 2.11
Node Version: 10
Npm Version: 6
Yarn Version: 1
javac 1.8.0_232 found
javac installed
JDK 1.8 found: javac 1.8.0_232
Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.16.6-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], NeatHTMLFeatures:[included:true, linearGradient:0], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
Final plugins [WebApollo:[included:true], NeatHTMLFeatures:[included:true, linearGradient:0], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
:installJBrowseWebOnly
JBrowse already exists
 * tag                 1.16.6-release -> FETCH_HEAD
Already up to date.
yarn install v1.21.1
warning package.json: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning package.json: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_run.js" (in "@gmod/jbrowse").
warning @gmod/jbrowse@1.16.6: Invalid bin entry for "jb_setup.js" (in "@gmod/jbrowse").
[1/4] Resolving packages...
[2/4] Fetching packages...
info fsevents@1.2.9: The platform "linux" is incompatible with this module.
info "fsevents@1.2.9" is an optional dependency and failed compatibility check. Excluding it from installation.
[3/4] Linking dependencies...
warning " > dojo-webpack-plugin@2.8.9" has unmet peer dependency "webpack-sources@>=1.0.1".
warning " > url-loader@0.5.7" has unmet peer dependency "file-loader@*".
[4/4] Building fresh packages...

Do you know is those warnings interfere in anything? And what about those one in steps [2/4] and [3/4]?


Is there anything I can do?

Thank you,

Luciano Kalabric.


De: Nathan Dunn <[hidden email]>
Enviado: segunda-feira, 6 de janeiro de 2020 16:17:27
Para: Scott Cain
Cc: Luciano Kalabric Silva; [hidden email]
Assunto: Re: [apollo] GMOD project
 

Luciano, I think we are all still here!

To use Apollo I recommend one of 4 solutions:

1 - Just get an account on the European use galaxy server.  They provide a JBrowse and an Apollo instance:  https://annotation.usegalaxy.eu/. It is free and no install required. 
3 - Load Apollo as an EC2 image from the AWS Marketplace.  We should have the most recent version (2.5.0) on the N. Virginia server)
4 - Install locally (what you are no doubt trying): https://genomearchitect.readthedocs.io/en/latest/Setup.html


If you need to install locally and its not working, please post any issues run into here on this mailing list.  (To sign up for the mailing list go here: https://groups.google.com/a/lbl.gov/forum/#!forum/apollo)

Cheers,

Nathan


On Jan 6, 2020, at 7:40 AM, Scott Cain <[hidden email]> wrote:

Hi Luciano,

I cc'ed the apollo mailing list--they might be able to help with getting Apollo installed.

Unfortunately, the GMOD in the Cloud server is the same age as the VirtualBox instance.  What are you interested in doing? Do you only want Apollo and JBrowse, or do you have something else in mind?  What kind of data do you have?

Scott



On Mon, Jan 6, 2020 at 9:08 AM Luciano Kalabric Silva <[hidden email]> wrote:
Hi Scott,
 
Good to know. I read you have an instance in the Cloud at AWS. I created an account there. How do I do to access GMOD in the Cloud? Is it free?
Since the VBox is not up-to-date, I do not know if my colleagues will allow me to make it available in our network (security issues).
 
I am trying to install Apollo and Jbrowse from scratch on Ubuntu Server 19.01 (64bits). I could do JBrowse and it seems to be working fine but Apollo is still giving me some problems! When I tried to deploy, it tried to check/install JBrowse again, if I am not mistaken. There are a couple of warnings I will try to figure out.
 
If possible, I would like to test GMOD. How do I do today?
 
Thanks for your prompt answer,
 
Luciano Kalabric.
 
 
 
De: Scott Cain <[hidden email]> 
Enviada em: segunda-feira, 6 de janeiro de 2020 13:50
Para: Luciano Kalabric Silva <[hidden email]>
Cc: [hidden email]
Assunto: Re: GMOD project
 
Hi Luciano,
 
Yes, the GMOD project is still active.  At around 2015, we went from two full time people working specifically on GMOD to a third of a person (me), but many of the core projects are still actively developed (Chado, Tripal, JBrowse, Apollo, Galaxy, and InterMine to name a few).  Unfortunately, I don't really have time to make a new VirtualBox instance, but I have toyed with the idea of recreating much of the same functionality with Docker, since most of the projects have docker files.
 
Please let me know if you have any questions,
Scott
 
 
On Mon, Jan 6, 2020 at 5:04 AM Luciano Kalabric Silva <[hidden email]> wrote:
Hi,
 
First of all, I would like to know if GMOD project is still active. I visited your web site and most things were up-to-date 2014. I am really interested to set up a server in my institution and I downloaded the VBox to test it. Unfortunately, most of the programs are old and I could not update them all! Is there any telephone or chat program we can use to communicate with you guys?
 
Thank,
 
Luciano Kalabric.


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

--
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].