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JAVA_HOME error, but it is set

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JAVA_HOME error, but it is set

Heleen
Hi,

I have been running apollo for a while now but wanted to test another instance with different database settings. I changed the config.groovy and then wanted to deploy but coudn't get a war file because it tells me JAVA_HOME is not set. But it is. And I've managed to install and deploy it before, so it confused me.

Now I am trying to do a fresh install on my laptop (so a different computer). I get the same error. I tried setting it in .profile with "", without "", with /, with /jre. But it won't run. Mysql and tomcat are running.

I am testing it with apollo run-local.

Any ideas on what is missing?

Also: will running 2 different instances (2 deploys) with a different production database work?

Thanks!
Heleen.

heleen@heleenubuntu:~/Apollo-2.0.6$ sudo ./apollo run-local
Grails not found using grailsw
Gradle not found using gradlew
javac 1.8.0_121 found
javac installed
JDK 1.8 found: javac 1.8.0_121
No log file found in classpath.
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 2.016 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

heleen@heleenubuntu:~/Apollo-2.0.6$ echo $JAVA_HOME
/usr/lib/jvm/java-1.8.0-openjdk-amd64





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Re: JAVA_HOME error, but it is set

nathandunn

You should build it without running sudo.  

In your Apollo directory I would do:

sudo chown -R heleen:heleen *  # sudo here is good, you need to change the permissions
./apollo clean-all   # no sudo 
./apollo run-local  # no sudo 

When running as sudo / root, most likely JAVA_HOME is not defined for root, which is why you’re getting the error, but I don’t think you want to build as root if you can help it. 

Nathan

On Apr 5, 2017, at 7:44 AM, Heleen <[hidden email]> wrote:

Hi,

I have been running apollo for a while now but wanted to test another instance with different database settings. I changed the config.groovy and then wanted to deploy but coudn't get a war file because it tells me JAVA_HOME is not set. But it is. And I've managed to install and deploy it before, so it confused me.

Now I am trying to do a fresh install on my laptop (so a different computer). I get the same error. I tried setting it in .profile with "", without "", with /, with /jre. But it won't run. Mysql and tomcat are running.

I am testing it with apollo run-local.

Any ideas on what is missing?

Also: will running 2 different instances (2 deploys) with a different production database work?

Thanks!
Heleen.

heleen@heleenubuntu:~/Apollo-2.0.6$ sudo ./apollo run-local
Grails not found using grailsw
Gradle not found using gradlew
javac 1.8.0_121 found
javac installed
JDK 1.8 found: javac 1.8.0_121
No log file found in classpath.
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 2.016 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

heleen@heleenubuntu:~/Apollo-2.0.6$ echo $JAVA_HOME
/usr/lib/jvm/java-1.8.0-openjdk-amd64




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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