TR: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

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TR: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

Isabel Marcelino-2

 

De : Isabel Marcelino [mailto:[hidden email]]
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after ./apollo run-local (with or without sudo)

 

Hello,

I am running MAKER and I would like to use Apollo to check on my results.

I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

 

Gradle not found using gradlew

javac 1.8.0_131 found

javac installed

JDK 1.8 found: javac 1.8.0_131

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

 

FAILURE: Build failed with an exception.

 

* What went wrong:

java.io.FileNotFoundException: /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)

> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)

 

When I use SUDO:

[hidden email] sudo ./apollo run-local

Grails not found using grailsw

Gradle not found using gradlew

javac 1.8.0_131 found

javac installed

JDK 1.8 found: javac 1.8.0_131

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

[ant:echo] Copying WebApollo plugin to jbrowse webapp ...

:setup-jbrowse

:copy-resources

:copyResourcesDev

found jbrowse directory false

Installing Perl prerequisites ...Prerequisites installed, finished.

:javac

:gwtc

 

BUILD SUCCESSFUL

 

Total time: 1 mins 2.031 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 (which is not right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

 

In any case, a temporary server is not automatically launched.

Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.

Thank you,

Isabel

 

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé

Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex

Guadeloupe, FWI

 

 




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www.avast.com






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Re: TR: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

nathandunn

What I would do is:

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
chown -R administrateur:administrateur *
./apollo run-local

Let me know how that works. 

Nathan


On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:

 
De : Isabel Marcelino [[hidden email]] 
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after ./apollo run-local (with or without sudo)
 
Hello,
I am running MAKER and I would like to use Apollo to check on my results. 
I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):
 
Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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
 
FAILURE: Build failed with an exception.
 
* What went wrong:
java.io.FileNotFoundException: /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
 
When I use SUDO:
[hidden email] sudo ./apollo run-local
Grails not found using grailsw
Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc
 
BUILD SUCCESSFUL
 
Total time: 1 mins 2.031 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 (which is not right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)
 
In any case, a temporary server is not automatically launched.
Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
Thank you,
Isabel
 
*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI
 
 



Avast logo

L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. 
www.avast.com


<a href="x-msg://4/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2" width="1" height="1" style="color: purple; text-decoration: underline;" class="">



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.

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RE: TR: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

Isabel Marcelino-2

Hi Nathan,

 

I had to use sudo to proceed with the command chown -R administrateur:administrateur *

After running ./apollo run-local, I get:

 

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6$ sudo chown -R administrateur:administrateur *

[sudo] password for x2go:

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6$ ./apollo run-local

Gradle not found using gradlew

javac 1.8.0_131 found

javac installed

JDK 1.8 found: javac 1.8.0_131

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

 

FAILURE: Build failed with an exception.

 

* What went wrong:

java.io.FileNotFoundException: /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)

> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)

 

* Try:

Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

 

BUILD FAILED

 

Total time: 5.831 secs

 

Thank you for your help,

Isabel

 

De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 25 August, 2017 2:25 PM
À : [hidden email]
Objet : Re: [apollo] TR: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

 

 

What I would do is:

 

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/

chown -R administrateur:administrateur *

./apollo run-local

 

Let me know how that works. 

 

Nathan

 

 

On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:

 

 

De : Isabel Marcelino [[hidden email]] 
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after ./apollo run-local (with or without sudo)

 

Hello,

I am running MAKER and I would like to use Apollo to check on my results. 

I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

 

Gradle not found using gradlew

javac 1.8.0_131 found

javac installed

JDK 1.8 found: javac 1.8.0_131

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

 

FAILURE: Build failed with an exception.

 

* What went wrong:

java.io.FileNotFoundException: /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)

> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)

 

When I use SUDO:

[hidden email] sudo ./apollo run-local

Grails not found using grailsw

Gradle not found using gradlew

javac 1.8.0_131 found

javac installed

JDK 1.8 found: javac 1.8.0_131

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

[ant:echo] Copying WebApollo plugin to jbrowse webapp ...

:setup-jbrowse

:copy-resources

:copyResourcesDev

found jbrowse directory false

Installing Perl prerequisites ...Prerequisites installed, finished.

:javac

:gwtc

 

BUILD SUCCESSFUL

 

Total time: 1 mins 2.031 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 (which is not right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

 

In any case, a temporary server is not automatically launched.

Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.

Thank you,

Isabel

 

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé

Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex

Guadeloupe, FWI

 

 

 

Avast logo

L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. 
www.avast.com






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: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

nathandunn

From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle
sudo chown -R administrateur:administrateur ~/.gradle
rm -rf ~/.gradle/caches/*

and then retry the deploy.

Nathan


> On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:
>
> Hi Nathan,
>  
> I had to use sudo to proceed with the command chown -R administrateur:administrateur *
> After running ./apollo run-local, I get:
>  
> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6$ sudo chown -R administrateur:administrateur *
> [sudo] password for x2go:
> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6$ ./apollo run-local
> Gradle not found using gradlew
> javac 1.8.0_131 found
> javac installed
> JDK 1.8 found: javac 1.8.0_131
> 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
>  
> FAILURE: Build failed with an exception.
>  
> * What went wrong:
> java.io.FileNotFoundException: /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
> > /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
>  
> * Try:
> Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
>  
> BUILD FAILED
>  
> Total time: 5.831 secs
>  
> Thank you for your help,
> Isabel
>  
> De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
> Envoyé : 25 August, 2017 2:25 PM
> À : [hidden email]
> Objet : Re: [apollo] TR: temporary server is not automatically launched after ./apollo run-local (with or without sudo)
>  
>  
> What I would do is:
>  
> cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
> chown -R administrateur:administrateur *
> ./apollo run-local
>  
> Let me know how that works.
>  
> Nathan
>  
>  
>> On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:
>>  
>>  
>> De : Isabel Marcelino [mailto:[hidden email]]
>> Envoyé : 25 August, 2017 12:36 PM
>> À : '[hidden email]'
>> Objet : temporary server is not automatically launched after ./apollo run-local (with or without sudo)
>>  
>> Hello,
>> I am running MAKER and I would like to use Apollo to check on my results.
>> I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):
>>  
>> Gradle not found using gradlew
>> javac 1.8.0_131 found
>> javac installed
>> JDK 1.8 found: javac 1.8.0_131
>> 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
>>  
>> FAILURE: Build failed with an exception.
>>  
>> * What went wrong:
>> java.io.FileNotFoundException: /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
>> > /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
>>  
>> When I use SUDO:
>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6$ sudo ./apollo run-local
>> Grails not found using grailsw
>> Gradle not found using gradlew
>> javac 1.8.0_131 found
>> javac installed
>> JDK 1.8 found: javac 1.8.0_131
>> 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
>> [ant:echo] Copying WebApollo plugin to jbrowse webapp ...
>> :setup-jbrowse
>> :copy-resources
>> :copyResourcesDev
>> found jbrowse directory false
>> Installing Perl prerequisites ...Prerequisites installed, finished.
>> :javac
>> :gwtc
>>  
>> BUILD SUCCESSFUL
>>  
>> Total time: 1 mins 2.031 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 (which is not right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)
>>  
>> In any case, a temporary server is not automatically launched.
>> Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
>> Thank you,
>> Isabel
>>  
>> *************************************************
>> Isabel MARCELINO, PhD
>> Unité Environnement Santé
>> Institut Pasteur de Guadeloupe
>> Morne Jolivière - B.P. 484
>> 97183 LES ABYMES Cedex
>> Guadeloupe, FWI
>>  
>>  
>>  
>>
>>
>> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
>> www.avast.com
>>
>>
>>
>>
>>
>> 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.

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RE: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

Isabel Marcelino-2
Hi Nathan,
I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
Thanks for your feedback.
Isabel

-----Message d'origine-----
De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 25 August, 2017 6:05 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle
sudo chown -R administrateur:administrateur ~/.gradle rm -rf ~/.gradle/caches/*

and then retry the deploy.

Nathan


> On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:
>
> Hi Nathan,
>
> I had to use sudo to proceed with the command chown -R
> administrateur:administrateur * After running ./apollo run-local, I get:
>
> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apol
> lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo] password for x2go:
> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apol
> lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
> 1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> java.io.FileNotFoundException:
> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
> dle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
> > /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
> > radle/2.11/taskArtifacts/cache.properties.lock (Permission non
> > accordée)
>
> * Try:
> Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
>
> BUILD FAILED
>
> Total time: 5.831 secs
>
> Thank you for your help,
> Isabel
>
> De : [hidden email]
> [mailto:[hidden email]] De la part de Nathan Dunn Envoyé
> : 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
> [apollo] TR: temporary server is not automatically launched after
> ./apollo run-local (with or without sudo)
>
>
> What I would do is:
>
> cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
> chown -R administrateur:administrateur * ./apollo run-local
>
> Let me know how that works.
>
> Nathan
>
>
>> On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:
>>
>>
>> De : Isabel Marcelino [mailto:[hidden email]]
>> Envoyé : 25 August, 2017 12:36 PM
>> À : '[hidden email]'
>> Objet : temporary server is not automatically launched after ./apollo
>> run-local (with or without sudo)
>>
>> Hello,
>> I am running MAKER and I would like to use Apollo to check on my results.
>> I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):
>>
>> Gradle not found using gradlew
>> javac 1.8.0_131 found
>> javac installed
>> JDK 1.8 found: javac 1.8.0_131
>> 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
>>
>> FAILURE: Build failed with an exception.
>>
>> * What went wrong:
>> java.io.FileNotFoundException:
>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
>> adle/2.11/taskArtifacts/cache.properties.lock (Permission non
>> accordée)
>> > /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
>> > gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
>> > accordée)
>>
>> When I use SUDO:
>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
>> llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw
>> Gradle not found using gradlew javac 1.8.0_131 found javac installed
>> JDK 1.8 found: javac 1.8.0_131 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
>> [ant:echo] Copying WebApollo plugin to jbrowse webapp ...
>> :setup-jbrowse
>> :copy-resources
>> :copyResourcesDev
>> found jbrowse directory false
>> Installing Perl prerequisites ...Prerequisites installed, finished.
>> :javac
>> :gwtc
>>
>> BUILD SUCCESSFUL
>>
>> Total time: 1 mins 2.031 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 (which is not
>> right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)
>>
>> In any case, a temporary server is not automatically launched.
>> Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
>> Thank you,
>> Isabel
>>
>> *************************************************
>> Isabel MARCELINO, PhD
>> Unité Environnement Santé
>> Institut Pasteur de Guadeloupe
>> Morne Jolivière - B.P. 484
>> 97183 LES ABYMES Cedex
>> Guadeloupe, FWI
>>
>>
>>
>>
>>
>> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
>> www.avast.com
>>
>>
>>
>>
>>
>> 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.


---
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus





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: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

nathandunn

You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.  

Nathan

> On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:
>
> Hi Nathan,
> I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
> I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
> Thanks for your feedback.
> Isabel
>
> -----Message d'origine-----
> De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
> Envoyé : 25 August, 2017 6:05 PM
> À : [hidden email]
> Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)
>
>
> From https://stackoverflow.com/a/37920679/1739366
>
> I would try:
>
> rm -rf /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gradle
> sudo chown -R administrateur:administrateur ~/.gradle rm -rf ~/.gradle/caches/*
>
> and then retry the deploy.
>
> Nathan
>
>
>> On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:
>>
>> Hi Nathan,
>>
>> I had to use sudo to proceed with the command chown -R
>> administrateur:administrateur * After running ./apollo run-local, I get:
>>
>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apol
>> lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo] password for x2go:
>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apol
>> lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
>> 1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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
>>
>> FAILURE: Build failed with an exception.
>>
>> * What went wrong:
>> java.io.FileNotFoundException:
>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
>> dle/2.11/taskArtifacts/cache.properties.lock (Permission non accordée)
>>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
>>> radle/2.11/taskArtifacts/cache.properties.lock (Permission non
>>> accordée)
>>
>> * Try:
>> Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
>>
>> BUILD FAILED
>>
>> Total time: 5.831 secs
>>
>> Thank you for your help,
>> Isabel
>>
>> De : [hidden email]
>> [mailto:[hidden email]] De la part de Nathan Dunn Envoyé
>> : 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
>> [apollo] TR: temporary server is not automatically launched after
>> ./apollo run-local (with or without sudo)
>>
>>
>> What I would do is:
>>
>> cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
>> chown -R administrateur:administrateur * ./apollo run-local
>>
>> Let me know how that works.
>>
>> Nathan
>>
>>
>>> On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:
>>>
>>>
>>> De : Isabel Marcelino [mailto:[hidden email]]
>>> Envoyé : 25 August, 2017 12:36 PM
>>> À : '[hidden email]'
>>> Objet : temporary server is not automatically launched after ./apollo
>>> run-local (with or without sudo)
>>>
>>> Hello,
>>> I am running MAKER and I would like to use Apollo to check on my results.
>>> I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):
>>>
>>> Gradle not found using gradlew
>>> javac 1.8.0_131 found
>>> javac installed
>>> JDK 1.8 found: javac 1.8.0_131
>>> 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
>>>
>>> FAILURE: Build failed with an exception.
>>>
>>> * What went wrong:
>>> java.io.FileNotFoundException:
>>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
>>> adle/2.11/taskArtifacts/cache.properties.lock (Permission non
>>> accordée)
>>>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
>>>> gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
>>>> accordée)
>>>
>>> When I use SUDO:
>>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
>>> llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw
>>> Gradle not found using gradlew javac 1.8.0_131 found javac installed
>>> JDK 1.8 found: javac 1.8.0_131 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
>>> [ant:echo] Copying WebApollo plugin to jbrowse webapp ...
>>> :setup-jbrowse
>>> :copy-resources
>>> :copyResourcesDev
>>> found jbrowse directory false
>>> Installing Perl prerequisites ...Prerequisites installed, finished.
>>> :javac
>>> :gwtc
>>>
>>> BUILD SUCCESSFUL
>>>
>>> Total time: 1 mins 2.031 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 (which is not
>>> right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)
>>>
>>> In any case, a temporary server is not automatically launched.
>>> Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
>>> Thank you,
>>> Isabel
>>>
>>> *************************************************
>>> Isabel MARCELINO, PhD
>>> Unité Environnement Santé
>>> Institut Pasteur de Guadeloupe
>>> Morne Jolivière - B.P. 484
>>> 97183 LES ABYMES Cedex
>>> Guadeloupe, FWI
>>>
>>>
>>>
>>>
>>>
>>> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
>>> www.avast.com
>>>
>>>
>>>
>>>
>>>
>>> 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.
>
>
>
> ---
> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
> https://www.avast.com/antivirus
>
>
>
>
> 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: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

Isabel Marcelino-2
Hi Nathan,
Here is the error log file.
Thank you for the help,
Isabel

-----Message d'origine-----
De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 12:13 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.

Nathan

> On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:
>
> Hi Nathan,
> I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
> I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
> Thanks for your feedback.
> Isabel
>
> -----Message d'origine-----
> De : [hidden email]
> [mailto:[hidden email]] De la part de Nathan Dunn Envoyé
> : 25 August, 2017 6:05 PM À : [hidden email] Objet : Re:
> [apollo] temporary server is not automatically launched after ./apollo
> run-local (with or without sudo)
>
>
> From https://stackoverflow.com/a/37920679/1739366
>
> I would try:
>
> rm -rf
> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
> dle sudo chown -R administrateur:administrateur ~/.gradle rm -rf
> ~/.gradle/caches/*
>
> and then retry the deploy.
>
> Nathan
>
>
>> On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:
>>
>> Hi Nathan,
>>
>> I had to use sudo to proceed with the command chown -R
>> administrateur:administrateur * After running ./apollo run-local, I get:
>>
>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
>> l lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo]
>> password for x2go:
>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
>> l lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
>> 1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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
>>
>> FAILURE: Build failed with an exception.
>>
>> * What went wrong:
>> java.io.FileNotFoundException:
>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
>> a dle/2.11/taskArtifacts/cache.properties.lock (Permission non
>> accordée)
>>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
>>> radle/2.11/taskArtifacts/cache.properties.lock (Permission non
>>> accordée)
>>
>> * Try:
>> Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
>>
>> BUILD FAILED
>>
>> Total time: 5.831 secs
>>
>> Thank you for your help,
>> Isabel
>>
>> De : [hidden email]
>> [mailto:[hidden email]] De la part de Nathan Dunn
>> Envoyé
>> : 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
>> [apollo] TR: temporary server is not automatically launched after
>> ./apollo run-local (with or without sudo)
>>
>>
>> What I would do is:
>>
>> cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
>> chown -R administrateur:administrateur * ./apollo run-local
>>
>> Let me know how that works.
>>
>> Nathan
>>
>>
>>> On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:
>>>
>>>
>>> De : Isabel Marcelino [mailto:[hidden email]]
>>> Envoyé : 25 August, 2017 12:36 PM
>>> À : '[hidden email]'
>>> Objet : temporary server is not automatically launched after
>>> ./apollo run-local (with or without sudo)
>>>
>>> Hello,
>>> I am running MAKER and I would like to use Apollo to check on my results.
>>> I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):
>>>
>>> Gradle not found using gradlew
>>> javac 1.8.0_131 found
>>> javac installed
>>> JDK 1.8 found: javac 1.8.0_131
>>> 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
>>>
>>> FAILURE: Build failed with an exception.
>>>
>>> * What went wrong:
>>> java.io.FileNotFoundException:
>>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
>>> r adle/2.11/taskArtifacts/cache.properties.lock (Permission non
>>> accordée)
>>>> /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
>>>> gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
>>>> accordée)
>>>
>>> When I use SUDO:
>>> x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Ap
>>> o llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw
>>> Gradle not found using gradlew javac 1.8.0_131 found javac installed
>>> JDK 1.8 found: javac 1.8.0_131 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
>>> [ant:echo] Copying WebApollo plugin to jbrowse webapp ...
>>> :setup-jbrowse
>>> :copy-resources
>>> :copyResourcesDev
>>> found jbrowse directory false
>>> Installing Perl prerequisites ...Prerequisites installed, finished.
>>> :javac
>>> :gwtc
>>>
>>> BUILD SUCCESSFUL
>>>
>>> Total time: 1 mins 2.031 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 (which is not
>>> right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)
>>>
>>> In any case, a temporary server is not automatically launched.
>>> Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
>>> Thank you,
>>> Isabel
>>>
>>> *************************************************
>>> Isabel MARCELINO, PhD
>>> Unité Environnement Santé
>>> Institut Pasteur de Guadeloupe
>>> Morne Jolivière - B.P. 484
>>> 97183 LES ABYMES Cedex
>>> Guadeloupe, FWI
>>>
>>>
>>>
>>>
>>>
>>> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
>>> www.avast.com
>>>
>>>
>>>
>>>
>>>
>>> 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.
>
>
>
> ---
> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
> https://www.avast.com/antivirus
>
>
>
>
> 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.


IM_apollo_grails.err.pdf (37K) Download Attachment
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Re: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

nathandunn

Isabel,

Either the mysql database is not on, or you don’t have the correct credentials in your apollo-config.groovy file.  


If you don’t have a preference, postgresql might be easier (we test it more):


Nathan

On Aug 28, 2017, at 10:19 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
Here is the error log file.
Thank you for the help,
Isabel

-----Message d'origine-----
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 12:13 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.

Nathan

On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
Thanks for your feedback.
Isabel

-----Message d'origine-----
De : [hidden email]
[[hidden email]] De la part de Nathan Dunn Envoyé
: 25 August, 2017 6:05 PM À : [hidden email] Objet : Re:
[apollo] temporary server is not automatically launched after ./apollo
run-local (with or without sudo)


From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
dle sudo chown -R administrateur:administrateur ~/.gradle rm -rf
~/.gradle/caches/*

and then retry the deploy.

Nathan


On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,

I had to use sudo to proceed with the command chown -R
administrateur:administrateur * After running ./apollo run-local, I get:

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo]
password for x2go:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
a dle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
radle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.831 secs

Thank you for your help,
Isabel

De : [hidden email]
[[hidden email]] De la part de Nathan Dunn
Envoyé
: 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
[apollo] TR: temporary server is not automatically launched after
./apollo run-local (with or without sudo)


What I would do is:

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
chown -R administrateur:administrateur * ./apollo run-local

Let me know how that works.

Nathan


On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:


De : Isabel Marcelino [[hidden email]]
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after
./apollo run-local (with or without sudo)

Hello,
I am running MAKER and I would like to use Apollo to check on my results.
I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
r adle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

When I use SUDO:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Ap
o llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw
Gradle not found using gradlew javac 1.8.0_131 found javac installed
JDK 1.8 found: javac 1.8.0_131 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
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 2.031 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 (which is not
right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

In any case, a temporary server is not automatically launched.
Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
Thank you,
Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI





L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
www.avast.com





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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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.



---
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus




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.


<IM_apollo_grails.err.pdf>


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: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

Isabel Marcelino-2

Hi Nathan,

I followed the instructions you sent me and the ones found in several webpages (concerning Apollo), either using either postgres or mysql databases, but somehow I do not manage to solve the problem.

Please find in attachment the error_log file from today with postgres. Regarding to the database “Apollo” I don’t have that in my postgres DB but I had it in mysqlDB. I have the feeling that, somehow, some file might have kept this information (is it possible?).

Thanks for your time and help,

Isabel

 

De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 7
:31 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)

 

 

Isabel,

 

Either the mysql database is not on, or you don’t have the correct credentials in your apollo-config.groovy file.  

 

 

If you don’t have a preference, postgresql might be easier (we test it more):

 

 

Nathan

 

On Aug 28, 2017, at 10:19 AM, Isabel Marcelino <[hidden email]> wrote:

 

Hi Nathan,
Here is the error log file.
Thank you for the help,
Isabel

-----Message d'origine-----
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 12:13 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.

Nathan


On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
Thanks for your feedback.
Isabel

-----Message d'origine-----
De : [hidden email]
[[hidden email]] De la part de Nathan Dunn Envoyé
: 25 August, 2017 6:05 PM À : [hidden email] Objet : Re:
[apollo] temporary server is not automatically launched after ./apollo
run-local (with or without sudo)


From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
dle sudo chown -R administrateur:administrateur ~/.gradle rm -rf
~/.gradle/caches/*

and then retry the deploy.

Nathan



On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,

I had to use sudo to proceed with the command chown -R
administrateur:administrateur * After running ./apollo run-local, I get:

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo]
password for x2go:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
a dle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
radle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)


* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.831 secs

Thank you for your help,
Isabel

De : [hidden email]
[[hidden email]] De la part de Nathan Dunn
Envoyé
: 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
[apollo] TR: temporary server is not automatically launched after
./apollo run-local (with or without sudo)


What I would do is:

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
chown -R administrateur:administrateur * ./apollo run-local

Let me know how that works.

Nathan



On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:


De : Isabel Marcelino [[hidden email]]
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after
./apollo run-local (with or without sudo)

Hello,
I am running MAKER and I would like to use Apollo to check on my results.
I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
r adle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)


When I use SUDO:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Ap
o llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw
Gradle not found using gradlew javac 1.8.0_131 found javac installed
JDK 1.8 found: javac 1.8.0_131 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
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 2.031 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 (which is not
right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

In any case, a temporary server is not automatically launched.
Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
Thank you,
Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI





L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
www.avast.com





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.




---
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus




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.


<IM_apollo_grails.err.pdf>


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.

 




Avast logo

L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
www.avast.com






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.


apollo_err_29aug2017.pdf (36K) Download Attachment
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Re: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

nathandunn
You need to do:

createdb apollo 

and then try restarting.   You may have to do that as the postgres user if you are using that. 

Nathan

On Aug 29, 2017, at 12:44 PM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
I followed the instructions you sent me and the ones found in several webpages (concerning Apollo), either using either postgres or mysql databases, but somehow I do not manage to solve the problem.
Please find in attachment the error_log file from today with postgres. Regarding to the database “Apollo” I don’t have that in my postgres DB but I had it in mysqlDB. I have the feeling that, somehow, some file might have kept this information (is it possible?).
Thanks for your time and help,
Isabel
 
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 7
:31 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)
 
 
Isabel,
 
Either the mysql database is not on, or you don’t have the correct credentials in your apollo-config.groovy file.  
 
 
If you don’t have a preference, postgresql might be easier (we test it more):
 
 
Nathan
 
On Aug 28, 2017, at 10:19 AM, Isabel Marcelino <[hidden email]> wrote:
 
Hi Nathan,
Here is the error log file.
Thank you for the help,
Isabel

-----Message d'origine-----
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 12:13 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.

Nathan


On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
Thanks for your feedback.
Isabel

-----Message d'origine-----
De : [hidden email] 
[[hidden email]] De la part de Nathan Dunn Envoyé 
: 25 August, 2017 6:05 PM À : [hidden email] Objet : Re: 
[apollo] temporary server is not automatically launched after ./apollo 
run-local (with or without sudo)


From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf 
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
dle sudo chown -R administrateur:administrateur ~/.gradle rm -rf 
~/.gradle/caches/*

and then retry the deploy.

Nathan



On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,

I had to use sudo to proceed with the command chown -R 
administrateur:administrateur * After running ./apollo run-local, I get:

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo] 
password for x2go:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
a dle/2.11/taskArtifacts/cache.properties.lock (Permission non 
accordée)

/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
radle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.831 secs

Thank you for your help,
Isabel

De : [hidden email]
[[hidden email]] De la part de Nathan Dunn 
Envoyé
: 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
[apollo] TR: temporary server is not automatically launched after 
./apollo run-local (with or without sudo)


What I would do is:

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
chown -R administrateur:administrateur * ./apollo run-local

Let me know how that works.

Nathan



On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:


De : Isabel Marcelino [[hidden email]]
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after 
./apollo run-local (with or without sudo)

Hello,
I am running MAKER and I would like to use Apollo to check on my results.
I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
r adle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

When I use SUDO:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Ap
o llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw 
Gradle not found using gradlew javac 1.8.0_131 found javac installed 
JDK 1.8 found: javac 1.8.0_131 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
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 2.031 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 (which is not 
right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

In any case, a temporary server is not automatically launched.
Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
Thank you,
Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI





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www.avast.com





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---
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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.


<IM_apollo_grails.err.pdf>


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www.avast.com


<a href="x-msg://1/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2" width="1" height="1" style="color: purple; text-decoration: underline;" class="">
<apollo_err_29aug2017.pdf>


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RE: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

Isabel Marcelino-2

I got in! Thank you so much Nathan !

Now I will try to load my results from MAKER and see how Apollo works.

Isabel

 

De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 29 August, 2017 4:11 PM
À : Apollo List
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)

 

You need to do:

 

createdb apollo 

 

and then try restarting.   You may have to do that as the postgres user if you are using that. 

 

Nathan

 

On Aug 29, 2017, at 12:44 PM, Isabel Marcelino <[hidden email]> wrote:

 

Hi Nathan,

I followed the instructions you sent me and the ones found in several webpages (concerning Apollo), either using either postgres or mysql databases, but somehow I do not manage to solve the problem.

Please find in attachment the error_log file from today with postgres. Regarding to the database “Apollo” I don’t have that in my postgres DB but I had it in mysqlDB. I have the feeling that, somehow, some file might have kept this information (is it possible?).

Thanks for your time and help,

Isabel

 

De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 7
:31 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)

 

 

Isabel,

 

Either the mysql database is not on, or you don’t have the correct credentials in your apollo-config.groovy file.  

 

 

If you don’t have a preference, postgresql might be easier (we test it more):

 

 

Nathan

 

On Aug 28, 2017, at 10:19 AM, Isabel Marcelino <[hidden email]> wrote:

 

Hi Nathan,
Here is the error log file.
Thank you for the help,
Isabel

-----Message d'origine-----
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 12:13 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.

Nathan



On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
Thanks for your feedback.
Isabel

-----Message d'origine-----
De : [hidden email] 
[[hidden email]] De la part de Nathan Dunn Envoyé 
: 25 August, 2017 6:05 PM À : [hidden email] Objet : Re: 
[apollo] temporary server is not automatically launched after ./apollo 
run-local (with or without sudo)


From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf 
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
dle sudo chown -R administrateur:administrateur ~/.gradle rm -rf 
~/.gradle/caches/*

and then retry the deploy.

Nathan




On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,

I had to use sudo to proceed with the command chown -R 
administrateur:administrateur * After running ./apollo run-local, I get:

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo] 
password for x2go:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
a dle/2.11/taskArtifacts/cache.properties.lock (Permission non 
accordée)


/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
radle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)


* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.831 secs

Thank you for your help,
Isabel

De : [hidden email]
[[hidden email]] De la part de Nathan Dunn 
Envoyé
: 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
[apollo] TR: temporary server is not automatically launched after 
./apollo run-local (with or without sudo)


What I would do is:

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
chown -R administrateur:administrateur * ./apollo run-local

Let me know how that works.

Nathan




On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:


De : Isabel Marcelino [[hidden email]]
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after 
./apollo run-local (with or without sudo)

Hello,
I am running MAKER and I would like to use Apollo to check on my results.
I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
r adle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)


/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)


When I use SUDO:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Ap
o llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw 
Gradle not found using gradlew javac 1.8.0_131 found javac installed 
JDK 1.8 found: javac 1.8.0_131 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
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 2.031 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 (which is not 
right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

In any case, a temporary server is not automatically launched.
Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
Thank you,
Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI





L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
www.avast.com





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.




---
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus




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.


<IM_apollo_grails.err.pdf>


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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<apollo_err_29aug2017.pdf>


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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: temporary server is not automatically launched after ./apollo run-local (with or without sudo)

nathandunn

Excellent.  Let us know if you have any further questions. 

Nathan


On Aug 30, 2017, at 6:33 AM, Isabel Marcelino <[hidden email]> wrote:

I got in! Thank you so much Nathan ! 
Now I will try to load my results from MAKER and see how Apollo works. 
Isabel
 
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 29 August, 2017 4:11 PM
À : Apollo List
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)
 
You need to do:
 
createdb apollo 
 
and then try restarting.   You may have to do that as the postgres user if you are using that. 
 
Nathan
 
On Aug 29, 2017, at 12:44 PM, Isabel Marcelino <[hidden email]> wrote:
 
Hi Nathan,
I followed the instructions you sent me and the ones found in several webpages (concerning Apollo), either using either postgres or mysql databases, but somehow I do not manage to solve the problem.
Please find in attachment the error_log file from today with postgres. Regarding to the database “Apollo” I don’t have that in my postgres DB but I had it in mysqlDB. I have the feeling that, somehow, some file might have kept this information (is it possible?).
Thanks for your time and help,
Isabel
 
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 7
:31 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)
 
 
Isabel,
 
Either the mysql database is not on, or you don’t have the correct credentials in your apollo-config.groovy file.  
 
 
If you don’t have a preference, postgresql might be easier (we test it more):
 
 
Nathan
 
On Aug 28, 2017, at 10:19 AM, Isabel Marcelino <[hidden email]> wrote:
 
Hi Nathan,
Here is the error log file.
Thank you for the help,
Isabel

-----Message d'origine-----
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 28 August, 2017 12:13 PM
À : [hidden email]
Objet : Re: [apollo] temporary server is not automatically launched after ./apollo run-local (with or without sudo)


You can continue on this thread and post any log files here.

They use a very similar set of methods, so weird that it is not working.

Nathan



On Aug 28, 2017, at 9:10 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,
I followed your suggestion and deleted all the files and folder that you mentioned and changed ownership of the Apollo 2.0.6 folder. I ran ./apollo deploy and I finally managed to create an Apollo WAR. Thank you!
I just ran ./apollo run-local and, after finding a suitable port, I have now a problem with Grails (and the temporary server is not automatically launched). Should I create another post for this issue or continue on this one?
Thanks for your feedback.
Isabel

-----Message d'origine-----
De : [hidden email] 
[[hidden email]] De la part de Nathan Dunn Envoyé 
: 25 August, 2017 6:05 PM À : [hidden email] Objet : Re: 
[apollo] temporary server is not automatically launched after ./apollo 
run-local (with or without sudo)


From https://stackoverflow.com/a/37920679/1739366

I would try:

rm -rf 
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gra
dle sudo chown -R administrateur:administrateur ~/.gradle rm -rf 
~/.gradle/caches/*

and then retry the deploy.

Nathan




On Aug 25, 2017, at 11:42 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan,

I had to use sudo to proceed with the command chown -R 
administrateur:administrateur * After running ./apollo run-local, I get:

x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ sudo chown -R administrateur:administrateur * [sudo] 
password for x2go:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apo
l lo-2.0.6$ ./apollo run-local Gradle not found using gradlew javac
1.8.0_131 found javac installed JDK 1.8 found: javac 1.8.0_131 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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.gr
a dle/2.11/taskArtifacts/cache.properties.lock (Permission non 
accordée)


/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
radle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.831 secs

Thank you for your help,
Isabel

De : [hidden email]
[[hidden email]] De la part de Nathan Dunn 
Envoyé
: 25 August, 2017 2:25 PM À : [hidden email] Objet : Re:
[apollo] TR: temporary server is not automatically launched after 
./apollo run-local (with or without sudo)


What I would do is:

cd /home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/
chown -R administrateur:administrateur * ./apollo run-local

Let me know how that works.

Nathan




On Aug 25, 2017, at 10:31 AM, Isabel Marcelino <[hidden email]> wrote:


De : Isabel Marcelino [[hidden email]]
Envoyé : 25 August, 2017 12:36 PM
À : '[hidden email]'
Objet : temporary server is not automatically launched after 
./apollo run-local (with or without sudo)

Hello,
I am running MAKER and I would like to use Apollo to check on my results.
I am trying to install Apollo-2.0.6 and, when I do not use “sudo”, I get this (sorry my message  is a bit long…):

Gradle not found using gradlew
javac 1.8.0_131 found
javac installed
JDK 1.8 found: javac 1.8.0_131
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

FAILURE: Build failed with an exception.

* What went wrong:
java.io.FileNotFoundException:
/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.g
r adle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)


/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Apollo-2.0.6/.
gradle/2.11/taskArtifacts/cache.properties.lock (Permission non
accordée)

When I use SUDO:
x2go@SRV-WGS:/home/administrateur/results/Isa/VIEWER_TOOLS/APOLLO/Ap
o llo-2.0.6$ sudo ./apollo run-local Grails not found using grailsw 
Gradle not found using gradlew javac 1.8.0_131 found javac installed 
JDK 1.8 found: javac 1.8.0_131 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
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 2.031 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 (which is not 
right because I set it to /usr/lib/jvm/java-8-openjdk-amd64/)

In any case, a temporary server is not automatically launched.
Could you please help me on that, as I ‘ve been trying to solve this issue for a couple of weeks now.
Thank you,
Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI





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