Apollo build process

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Apollo build process

darren.hart@otago.ac.nz

Hi,

 

Im trying to do a build of the newest Apollo (see below) it appears to build correctly and says it has been successful but there is no war file generated in the target directory. Is there anything I’m doing wrong indicated by the results below?

 

Thanks

 

Darren

 

[itadmin@thehive Apollo-2.0.6]$ sudo ./apollo deploy

which: no grails in (/sbin:/bin:/usr/sbin:/usr/bin)

which: no gradle in (/sbin:/bin:/usr/sbin:/usr/bin)

Grails not found using grailsw

Gradle not found using gradlew

javac 1.8.0_121 found

javac installed

JDK 1.8 found: javac 1.8.0_121

final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]

Copying apollo plugin

handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

:evaluateJBrowseConfigs UP-TO-DATE

:installJBrowse

installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

:copyApolloPlugin UP-TO-DATE

:installJBrowsePlugins

installing jbrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]

Evaluating plugin WebApollo=[included:true]

Plugin jbrowse-download/plugins/WebApollo exists and appears valid.

Evaluating plugin RegexSequenceSearch=[included:true]

Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid.

Evaluating plugin HideTrackLabels=[included:true]

Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid.

:handleJBrowse

:copy.apollo.plugin.webapp

:setup-jbrowse

:copy-resources

:javac

:gwtc

 

BUILD SUCCESSFUL

 

Total time: 35.573 secs

 

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html

grailsw: JAVA_HOME environment variable is not set

***************************************

NOTE: Please set the memory for your servlet container (tomcat, jetty, etc.) or Apollo may not start correctly: http://genomearchitect.readthedocs.io/en/latest/Troubleshooting/#tomcat-memory

 

Darren Hart | IT Manager | Department of Biochemistry | University of Otago

T - +6434794965 | M - +6421991638





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

nathandunn

If it uses gradlew or grailsw (where it automatically downloads these) you need to define JAVA_HOME:


e.g.

export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/  # or set in .bashrc / .project
I created an issue so that we require during the build phase if using either grailsw or gradlew and indicate you need to do this (as it is a common error). 

Nathan

On Feb 16, 2017, at 3:06 AM, Darren Hart <[hidden email]> wrote:

Hi,
 
Im trying to do a build of the newest Apollo (see below) it appears to build correctly and says it has been successful but there is no war file generated in the target directory. Is there anything I’m doing wrong indicated by the results below?
 
Thanks
 
Darren
 
[itadmin@thehive Apollo-2.0.6]$ sudo ./apollo deploy
which: no grails in (/sbin:/bin:/usr/sbin:/usr/bin)
which: no gradle in (/sbin:/bin:/usr/sbin:/usr/bin)
Grails not found using grailsw
Gradle not found using gradlew
javac 1.8.0_121 found
javac installed
JDK 1.8 found: javac 1.8.0_121
final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Copying apollo plugin
handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:copyApolloPlugin UP-TO-DATE
:installJBrowsePlugins
installing jbrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse-download/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid.
:handleJBrowse
:copy.apollo.plugin.webapp
:setup-jbrowse
:copy-resources
:javac
:gwtc
 
BUILD SUCCESSFUL
 
Total time: 35.573 secs
 
This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
grailsw: JAVA_HOME environment variable is not set
***************************************
NOTE: Please set the memory for your servlet container (tomcat, jetty, etc.) or Apollo may not start correctly: http://genomearchitect.readthedocs.io/en/latest/Troubleshooting/#tomcat-memory
 
Darren Hart | IT Manager | Department of Biochemistry | University of Otago
T - +6434794965 | M - +6421991638



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: Apollo build process

darren.hart@otago.ac.nz

Hi Nathan,

 

Thanks for the tip, that was the reason, all built and running now. It was using my built version of grails but gradle was being downloaded and built during install.

 

Cheers,

 

Darren Hart | IT Manager | Department of Biochemistry | University of Otago

T - +6434794965 | M - +6421991638

 

From: <[hidden email]> on behalf of Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Friday, 17 February 2017 at 5:38 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] Apollo build process

 

 

If it uses gradlew or grailsw (where it automatically downloads these) you need to define JAVA_HOME:

 

 

e.g.

 

export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/  # or set in .bashrc / .project

I created an issue so that we require during the build phase if using either grailsw or gradlew and indicate you need to do this (as it is a common error). 

 

Nathan

 

On Feb 16, 2017, at 3:06 AM, Darren Hart <[hidden email]> wrote:

 

Hi,

 

Im trying to do a build of the newest Apollo (see below) it appears to build correctly and says it has been successful but there is no war file generated in the target directory. Is there anything I’m doing wrong indicated by the results below?

 

Thanks

 

Darren

 

[itadmin@thehive Apollo-2.0.6]$ sudo ./apollo deploy

which: no grails in (/sbin:/bin:/usr/sbin:/usr/bin)

which: no gradle in (/sbin:/bin:/usr/sbin:/usr/bin)

Grails not found using grailsw

Gradle not found using gradlew

javac 1.8.0_121 found

javac installed

JDK 1.8 found: javac 1.8.0_121

final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]

Copying apollo plugin

handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

:evaluateJBrowseConfigs UP-TO-DATE

:installJBrowse

installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:29795a1bbb8da4706eba2b0f73724ac1b3e1e4e6, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]

:copyApolloPlugin UP-TO-DATE

:installJBrowsePlugins

installing jbrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]

Evaluating plugin WebApollo=[included:true]

Plugin jbrowse-download/plugins/WebApollo exists and appears valid.

Evaluating plugin RegexSequenceSearch=[included:true]

Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid.

Evaluating plugin HideTrackLabels=[included:true]

Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid.

:handleJBrowse

:copy.apollo.plugin.webapp

:setup-jbrowse

:copy-resources

:javac

:gwtc

 

BUILD SUCCESSFUL

 

Total time: 35.573 secs

 

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html

grailsw: JAVA_HOME environment variable is not set

***************************************

NOTE: Please set the memory for your servlet container (tomcat, jetty, etc.) or Apollo may not start correctly: http://genomearchitect.readthedocs.io/en/latest/Troubleshooting/#tomcat-memory

 

Darren Hart | IT Manager | Department of Biochemistry | University of Otago

T - +6434794965 | M - +6421991638




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.