I am installing web apollo software using following commnd.
sudo ./apollo run-local 8086
It seems build is successul but i cannot see webappolo at http://localhost:8086/apollo.
Grails not found using grailsw
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:99d8e6e1e7dfe290b839d41c18f41cf92d9afc7c, 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]]
The Task.leftShift(Closure) method has been deprecated and is scheduled to be removed in Gradle 5.0. Please use Task.doLast(Action) instead.
at build_9fqhqvhf4dstyctesvjrw31cc.run(/home/manish/Desktop/Apollo/build.gradle:102)
Copying apollo plugin
handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:99d8e6e1e7dfe290b839d41c18f41cf92d9afc7c, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:99d8e6e1e7dfe290b839d41c18f41cf92d9afc7c, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
npm WARN npm npm does not support Node.js v0.10.25
npm WARN npm You should probably upgrade to a newer version of node as we
npm WARN npm can't make any promises that npm will work with this version.
npm WARN npm You can find the latest version at https://nodejs.org/
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:99d8e6e1e7dfe290b839d41c18f41cf92d9afc7c, 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: 47.285 secs
grailsw: JAVA_HOME environment variable is not set
I checked following dependencies already installed.
$ node -v
v0.10.25
$ java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
How can i fix above error?
•
written
by
mandecent.gupta •
1 answer
Just adding as an answer instead of comment:
I think what it boils down to is that sudo uses a different "environment variables" so even though JAVA_HOME is part of your current user installation, it is not part of the sudo user, so it fails. You should probably run this command without sudo if possible, or make JAVA_HOME a part of your sudo user's environment. Ref http://gmod.827538.n3.nabble.com/JAVA-HOME-error-but-it-is-set-td4057418.html
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Based on the error I guess you need to set the environmental variable $JAVA_HOME, the directory in which you installed java.
i set the path using following command.
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64 Also i checked
echo $JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64
but still same error.
Please use
ADD COMMENTorADD REPLYto answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.Thanks for your advice. Can you pls help me in fixing my error.
I would recommend sending an email to their mailing list apollo@lists.lbl.gov
Also there have been several other recent threads in their mailing list archive here discussing this issue that might be of use http://gmod.827538.n3.nabble.com/Apollo-f815553.html
I think what it boils down to is that sudo uses a different "environment variables" so even though JAVA_HOME is part of your current user installation, it is not part of the sudo user, so it fails. You should probably run this command without sudo if possible, or make JAVA_HOME a part of your sudo user's environment. Ref http://gmod.827538.n3.nabble.com/JAVA-HOME-error-but-it-is-set-td4057418.html