Closed sbmimi closed 8 years ago
nathandunn
commented
8 years ago Thanks for finding this bug. We'll try to get this fixed (thought it was working). It might be that the jbrowse requirements are not yet installed, but I'll have to see.
Either way, I would probably suggest using the 2.0.2 version which has been thoroughly tested in the interim unless you need a specific feature of the up-coming release.
cmdcolin
commented
8 years ago This is probably due to watchman having the wrong permissions
I would probably just take away the watchman setup for all the commands and only do it on demand
nathandunn
commented
8 years ago @sbmimi I wasn't able to reproduce it, but @cmdcolin thinks he might have a fix. I pulled it in if you want to retry it. If you don't and just want to use 2.0.2 instead that is fine. Either way thanks for reporting.
cmdcolin
commented
8 years ago yep. I would first rm -rf web-app/jbrowse and then do another apollo run-local hope that helps!
sbmimi
commented
8 years ago @cmdcolin I tried to remove web-app/jbrowse then re-run and I am getting the same error. How can I change the permissions of the watchman?
Also, I am using 2.0.2 now and this is the error I'm getting when running ./apollo run-local:
ResNet-30-241:Apollo-2.0.2 mimiyxu$ ./apollo run-local Buildfile: /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml
copy.apollo.plugin.webapp: [echo] Copying WebApollo plugin to jbrowse webapp ...
setup-jbrowse:
copy-resources:
javac:
[javac] Compiling 63 source files to /Users/mimiyxu/Downloads/Apollo-2.0.2/target/classes/gwt
[javac] javac: invalid target release: 1.7
[javac] Usage: javac
BUILD FAILED /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml:26: Compile failed; see the compiler error output for details.
Total time: 0 seconds ResNet-30-241:Apollo-2.0.2 mimiyxu$ rm -rf web-app/jbrowse/ ResNet-30-241:Apollo-2.0.2 mimiyxu$ ./apollo run-local Buildfile: /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml
copy.apollo.plugin.webapp:
setup-jbrowse:
git.clone:
copy.apollo.plugin.jbrowse: [echo] copying plugin to jbrowse git ... [echo] Will be setting up jbrowse [copy] Copying 10405 files to /Users/mimiyxu/Downloads/Apollo-2.0.2/web-app/jbrowse
install.jbrowse.perl:
copy-resources:
javac:
[javac] Compiling 63 source files to /Users/mimiyxu/Downloads/Apollo-2.0.2/target/classes/gwt
[javac] javac: invalid target release: 1.7
[javac] Usage: javac
BUILD FAILED /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml:26: Compile failed; see the compiler error output for details.
Total time: 12 seconds
Thank you so much for your help!
nathandunn
commented
8 years ago If you type “java -version” or “javac -version”
what do you see?
Also, what system are you on?
You should be able to compile using java 1.8 (the default).
Nathan
On May 3, 2016, at 11:47 PM, sbmimi notifications@github.com wrote:
@cmdcolin https://github.com/cmdcolin I tried to remove web-app/jbrowse then re-run and I am getting the same error. How can I change the permissions of the watchman?
Also, I am using 2.0.2 now and this is the error I'm getting when running ./apollo run-local:
ResNet-30-241:Apollo-2.0.2 mimiyxu$ ./apollo run-local Buildfile: /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml
copy.apollo.plugin.webapp: [echo] Copying WebApollo plugin to jbrowse webapp ...
setup-jbrowse:
copy-resources:
javac: [javac] Compiling 63 source files to /Users/mimiyxu/Downloads/Apollo-2.0.2/target/classes/gwt [javac] javac: invalid target release: 1.7 [javac] Usage: javac [javac] use -help for a list of possible options
BUILD FAILED /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml:26: Compile failed; see the compiler error output for details.
Total time: 0 seconds ResNet-30-241:Apollo-2.0.2 mimiyxu$ rm -rf web-app/jbrowse/ ResNet-30-241:Apollo-2.0.2 mimiyxu$ ./apollo run-local Buildfile: /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml
copy.apollo.plugin.webapp:
setup-jbrowse:
git.clone:
copy.apollo.plugin.jbrowse: [echo] copying plugin to jbrowse git ... [echo] Will be setting up jbrowse [copy] Copying 10405 files to /Users/mimiyxu/Downloads/Apollo-2.0.2/web-app/jbrowse
install.jbrowse.perl:
copy-resources:
javac: [javac] Compiling 63 source files to /Users/mimiyxu/Downloads/Apollo-2.0.2/target/classes/gwt [javac] javac: invalid target release: 1.7 [javac] Usage: javac [javac] use -help for a list of possible options
BUILD FAILED /Users/mimiyxu/Downloads/Apollo-2.0.2/build.xml:26: Compile failed; see the compiler error output for details.
Total time: 12 seconds
Thank you so much for your help!
— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/1017#issuecomment-216759772
sbmimi
commented
8 years ago @nathandunn java version "1.6.0_65" Java(TM) SE Runtime Environment (build 1.6.0_65-b14-468-11M4833) Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-468, mixed mode)
I am on a MacBook Pro OS X Yosemite
cmdcolin
commented
8 years ago It will need at least java 1.7 (also known as just java 7) to compile right http://webapollo.readthedocs.io/en/latest/Prerequisites.html
You can try getting java 7 or java 8 from oracle or similar! You could try installing it from oracle and then running java -version again to see if it upgraded correctly
nathandunn
commented
8 years ago Ahh . . yeah, you’ll want to install Java 7 or Java 8.
You can use home-brew (OpenJDK is okay) or install the JDK (which will install the JRE as well) directly from Oracle.
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
Once installed you may need to set the JAVA_HOME variable. I use a script like this (running OS X 10.9.5), but it might just work:
https://stackoverflow.com/questions/26252591/mac-os-x-and-multiple-java-versions/32662139#32662139 https://stackoverflow.com/questions/26252591/mac-os-x-and-multiple-java-versions/32662139#32662139
Nathan
On May 4, 2016, at 1:15 PM, sbmimi notifications@github.com wrote:
@nathandunn https://github.com/nathandunn java version "1.6.0_65" Java(TM) SE Runtime Environment (build 1.6.0_65-b14-468-11M4833) Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-468, mixed mode)
I am on a MacBook Pro OS X Yosemite
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/1017#issuecomment-216988125
sbmimi
commented
8 years ago Hey!
So I set the JAVA_HOME variable and I was able to run the ./apollo run-local command. Doing so would prompt a whole bunch of text and finally end with BUILD SUCCESSFUL. However, after this, it starts trying to access grails. In the quickstart guide, there was an instruction to set the grails version to 2.4.5, however, the program complains:
"Application expects grails version [2.5.4], but GRAILS_HOME is version [2.4.5] - use the correct Grails version or run 'grails set-grails-version' if this Grails version is newer than the version your application expects."
I then upgraded my grails version to 2.5.4 and re-ran ./apollo run-local. Once again, after the build succeeded, grails once again complained saying:
"Application expects grails version [2.4.5], but GRAILS_HOME is version [2.5.4] - use the correct Grails version or run 'grails set-grails-version' if this Grails version is newer than the version your application expects."
As a last resort, I tried grails set-grails-version 2.4.5 and I got the same error detailed in the top of this post.
Any advice?
Thank you!
nathandunn
commented
8 years ago If you are pulling from master, you need the grails version 2.5.4 or just remove it and it will download the correct version.
If you are using sdkman you do:
sdk install grails 2.5.4
or just remove grails and it will automatically download the correct version.
Nathan
On May 11, 2016, at 6:18 PM, sbmimi notifications@github.com wrote:
Hey!
So I set the JAVA_HOME variable and I was able to run the ./apollo run-local command. Doing so would prompt a whole bunch of text and finally end with BUILD SUCCESSFUL. However, after this, it starts trying to access grails. In the quickstart guide, there was an instruction to set the grails version to 2.4.5, however, the program complains:
"Application expects grails version [2.5.4], but GRAILS_HOME is version [2.4.5] - use the correct Grails version or run 'grails set-grails-version' if this Grails version is newer than the version your application expects."
I then upgraded my grails version to 2.5.4 and re-ran ./apollo run-local. Once again, after the build succeeded, grails once again complained saying:
"Application expects grails version [2.4.5], but GRAILS_HOME is version [2.5.4] - use the correct Grails version or run 'grails set-grails-version' if this Grails version is newer than the version your application expects."
As a last resort, I tried grails set-grails-version 2.4.5 and I got the same error detailed in the top of this post.
Any advice?
Thank you!
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/1017#issuecomment-218635011
nathandunn
commented
8 years ago Though, I would use 2.0.2 (currently running Grails 2.4.5).
https://github.com/GMOD/Apollo/releases/tag/2.0.2 https://github.com/GMOD/Apollo/releases/tag/2.0.2
Nathan
On May 11, 2016, at 6:18 PM, sbmimi notifications@github.com wrote:
Hey!
So I set the JAVA_HOME variable and I was able to run the ./apollo run-local command. Doing so would prompt a whole bunch of text and finally end with BUILD SUCCESSFUL. However, after this, it starts trying to access grails. In the quickstart guide, there was an instruction to set the grails version to 2.4.5, however, the program complains:
"Application expects grails version [2.5.4], but GRAILS_HOME is version [2.4.5] - use the correct Grails version or run 'grails set-grails-version' if this Grails version is newer than the version your application expects."
I then upgraded my grails version to 2.5.4 and re-ran ./apollo run-local. Once again, after the build succeeded, grails once again complained saying:
"Application expects grails version [2.4.5], but GRAILS_HOME is version [2.5.4] - use the correct Grails version or run 'grails set-grails-version' if this Grails version is newer than the version your application expects."
As a last resort, I tried grails set-grails-version 2.4.5 and I got the same error detailed in the top of this post.
Any advice?
Thank you!
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/1017#issuecomment-218635011
Hi everyone,
I'm very new to Apollo and command line installation, so please bear with me. I am trying to download Apollo using the quick-start guide here: http://webapollo.readthedocs.io/en/latest/Apollo2Build.html
I have downloaded everything until the step that says "Verify install requirements" by using the command line ./apollo run-local. I receive an error that says:
"Grails not found using grailsw Gradle not found using gradlew Defining custom 'build' task when using the standard Gradle lifecycle plugins has been deprecated and is scheduled to be removed in Gradle 3.0 Defining custom 'clean' task when using the standard Gradle lifecycle plugins has been deprecated and is scheduled to be removed in Gradle 3.0 No log file found in classpath. final JBrowse settings [git:[url:https://github.com/GMOD/jbrowse, branch:master, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] final plugins [WebApollo:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]] Copying apollo plugin handling jbrowse release [git:[url:https://github.com/GMOD/jbrowse, branch:master, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] handling jbrowse [git:[url:https://github.com/GMOD/jbrowse, branch:master, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] :evaluateJBrowseConfigs UP-TO-DATE :installJBrowse installing jbrowse [git:[url:https://github.com/GMOD/jbrowse, branch:master, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] checkout out branch master Out: Already on 'master' Your branch is behind 'origin/master' by 58 commits, and can be fast-forwarded. (use "git pull" to update your local branch)
Pulling https://github.com/GMOD/jbrowse git pull /Users/mimiyxu/Apollo/jbrowse-download Out: Updating 1bac96a..61bc96f Fast-forward .travis.yml | 9 +- ChangeLog.md | 2 +- README.md | 6 +- apollo | 68 +- application.properties | 5 +- build.gradle | 69 +- build.xml | 11 +- client/apollo/js/View/Dialog/Help.js | 2 +- client/apollo/js/View/Track/AnnotTrack.js | 489 +++++-- client/apollo/js/View/Track/AnnotTrackSocket.js | 248 ---- client/apollo/js/View/Track/SequenceTrack.js | 3 +- client/apollo/js/main.js | 6 +- docs/ChadoExport.md | 6 +- docs/Configure.md | 2 +- docs/TestScript.md | 2 +- .../suite2/jmeter-dev-stress-test-notes.md | 4 +- docs/index.rst | 5 +- .../examples/groovy/SampleFeatures.groovy | 11 +- docs/web_services/examples/groovy/get_gff3.groovy | 1 - grails-app/conf/BootStrap.groovy | 8 + grails-app/conf/BuildConfig.groovy | 7 +- grails-app/conf/Config.groovy | 8 +- grails-app/conf/DataSource.groovy | 9 +- grails-app/conf/UrlMappings.groovy | 21 +- .../conf/org/bbop/apollo/SecurityFilters.groovy | 14 +- .../bbop/apollo/AnnotationEditorController.groovy | 53 +- .../org/bbop/apollo/AnnotatorController.groovy | 57 +- .../org/bbop/apollo/FeatureEventController.groovy | 3 +- .../org/bbop/apollo/GroupController.groovy | 231 ++- .../org/bbop/apollo/HomeController.groovy | 6 +- .../org/bbop/apollo/IOServiceController.groovy | 159 +- .../org/bbop/apollo/JbrowseController.groovy | 198 +-- .../org/bbop/apollo/OrganismController.groovy | 11 +- .../org/bbop/apollo/SequenceController.groovy | 17 +- .../org/bbop/apollo/UserController.groovy | 67 +- .../domain/org/bbop/apollo/Preference.groovy | 6 + .../org/bbop/apollo/UserOrganismPreference.groovy | 3 +- ...angelog-2.0.0.groovy => changelog-2_0_0.groovy} | 0 ...angelog-2.0.1.groovy => changelog-2_0_1.groovy} | 0 ...angelog-2.0.2.groovy => changelog-2_0_2.groovy} | 0 ...angelog-2.0.3.groovy => changelog-2_0_3.groovy} | 0 grails-app/migrations/changelog.groovy | 6 +- .../org/bbop/apollo/AnnotatorService.groovy | 9 +- .../org/bbop/apollo/ChadoHandlerService.groovy | 18 +- .../services/org/bbop/apollo/ExonService.groovy | 6 +- .../org/bbop/apollo/FeatureEventService.groovy | 26 +- .../bbop/apollo/FeatureRelationshipService.groovy | 67 +- .../services/org/bbop/apollo/FeatureService.groovy | 413 +++++- .../apollo/NonCanonicalSplitSiteService.groovy | 57 +- .../org/bbop/apollo/PermissionService.groovy | 214 ++- .../org/bbop/apollo/PreferenceService.groovy | 183 ++- .../org/bbop/apollo/RequestHandlingService.groovy | 152 +- grails-app/views/annotator/index.gsp | 1 + grails-app/views/auth/login.gsp | 93 +- .../views/jbrowse/chooseOrganismForJbrowse.gsp | 2 +- grails-app/views/layouts/login.gsp | 107 ++ grailsw | 8 +- grailsw.bat | 8 +- restapidoc.json | 1538 ++++++++++---------- sample-h2-apollo-config.groovy | 37 +- sample-mysql-apollo-config.groovy | 46 +- sample-postgres-apollo-config.groovy | 92 +- .../chado-schema-with-ontologies.sql.gz | Bin .../bbop/apollo/history/FeatureOperation.groovy | 3 +- src/gwt/org/bbop/apollo/gwt/client/Annotator.java | 77 +- .../org/bbop/apollo/gwt/client/AnnotatorPanel.java | 19 +- src/gwt/org/bbop/apollo/gwt/client/GroupPanel.java | 13 +- .../org/bbop/apollo/gwt/client/GroupPanel.ui.xml | 2 +- src/gwt/org/bbop/apollo/gwt/client/MainPanel.java | 44 +- .../apollo/gwt/client/ReferenceSequenceOracle.java | 9 +- .../org/bbop/apollo/gwt/client/resources/Table.css | 3 +- .../bbop/apollo/gwt/client/rest/RestService.java | 8 + .../apollo/gwt/shared/ClientTokenGenerator.java | 30 + .../bbop/apollo/gwt/shared/FeatureStringEnum.java | 2 + src/templates/war/web.xml | 82 ++ test/config/mysql.travis | 9 + test/config/postgres.travis | 6 +- .../bbop/apollo/CdsServiceIntegrationSpec.groovy | 9 +- .../ChadoHandlerServiceIntegrationSpec.groovy | 7 +- ...eatureRelationshipServiceIntegrationSpec.groovy | 29 + .../apollo/FeatureServiceIntegrationSpec.groovy | 135 ++ .../Gff3HandlerServiceIntegrationSpec.groovy | 10 +- .../apollo/OverlapperServiceIntegrationSpec.groovy | 30 +- .../RequestHandlingServiceIntegrationSpec.groovy | 340 ++++- .../apollo/SequenceServiceIntegrationSpec.groovy | 4 +- .../org/bbop/apollo/PermissionServiceSpec.groovy | 6 +- web-app/js/restapidoc/restapidoc.json | 1538 ++++++++++---------- ...-2.4.3.jar => grails-wrapper-runtime-2.4.5.jar} | Bin 6185 -> 6185 bytes wrapper/grails-wrapper-runtime-2.5.4.jar | Bin 0 -> 6110 bytes wrapper/grails-wrapper.properties | 2 +- wrapper/springloaded-1.2.0.RELEASE.jar | Bin 412416 -> 0 bytes wrapper/springloaded-1.2.3.RELEASE.jar | Bin 0 -> 419159 bytes wrapper/springloaded-1.2.4.RELEASE.jar | Bin 0 -> 427010 bytes 93 files changed, 4135 insertions(+), 3192 deletions(-) delete mode 100644 client/apollo/js/View/Track/AnnotTrackSocket.js rename grails-app/migrations/{changelog-2.0.0.groovy => changelog-2_0_0.groovy} (100%) rename grails-app/migrations/{changelog-2.0.1.groovy => changelog-2_0_1.groovy} (100%) rename grails-app/migrations/{changelog-2.0.2.groovy => changelog-2_0_2.groovy} (100%) rename grails-app/migrations/{changelog-2.0.3.groovy => changelog-2_0_3.groovy} (100%) create mode 100644 grails-app/views/layouts/login.gsp rename chado-schema-with-ontologies.sql.gz => scripts/chado-schema-with-ontologies.sql.gz (100%) create mode 100644 src/gwt/org/bbop/apollo/gwt/shared/ClientTokenGenerator.java create mode 100644 src/templates/war/web.xml rename wrapper/{grails-wrapper-runtime-2.4.3.jar => grails-wrapper-runtime-2.4.5.jar} (86%) create mode 100644 wrapper/grails-wrapper-runtime-2.5.4.jar delete mode 100644 wrapper/springloaded-1.2.0.RELEASE.jar create mode 100644 wrapper/springloaded-1.2.3.RELEASE.jar create mode 100644 wrapper/springloaded-1.2.4.RELEASE.jar
:copyApolloPlugin :installJBrowsePlugins installing jbrowse plugins [WebApollo:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]] Evaluating plugin WebApollo=[included:true] Plugin jbrowse-download/plugins/WebApollo exists and appears valid. Evaluating plugin NeatHTMLFeatures=[included:true] Plugin jbrowse-download/plugins/NeatHTMLFeatures exists and appears valid. Evaluating plugin NeatCanvasFeatures=[included:true] Plugin jbrowse-download/plugins/NeatCanvasFeatures exists and appears valid. Evaluating plugin RegexSequenceSearch=[included:true] Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid. Evaluating plugin HideTrackLabels=[included:true] Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid. :handleJBrowse :copy.apollo.plugin.webapp :setup-jbrowse [ant:exec] Result: 128 [ant:exec] Result: 1 [ant:echo] copying plugin to jbrowse git ... [ant:echo] Will be setting up jbrowse :setup-jbrowse FAILED
FAILURE: Build failed with an exception.
What went wrong: Execution failed for task ':setup-jbrowse'.
BUILD FAILED
Total time: 41.802 secs { "version": "4.4.0", "triggerid": "jsfilescopy", "disposition": "already_defined" }"
I'd really like some help on what I should do. I have no background in computer science or anything relating to coding, so I have no idea what exactly failed and how I should proceed.
Thank you for reading! I'd really want to use Apollo!!