Build file '/apollo/build.gradle' line: 321

[mictadlo]

Hi @erasche,
I updated Apollo in your dockerfile (erasche/docker-apollo) ENV WEBAPOLLO_VERSION 6189ff9e2973e1523ddcdbeee9d258c435c42a54 but the build failed:

$ docker-compose up
Building apollo
Step 1/8 : FROM tomcat:8.5-jre8-alpine
8.5-jre8-alpine: Pulling from library/tomcat
8e3ba11ec2a2: Pull complete
311ad0da4533: Pull complete
391a6a6b3651: Pull complete
b019068f0374: Pull complete
4af2bc8629f4: Pull complete
47b50a450cc9: Pull complete
Digest: sha256:ff9b220a0e311c29e12a85163fce690d90c0d33bcc8bf532fd25a6a0d9b43ddb
Status: Downloaded newer image for tomcat:8.5-jre8-alpine
 ---> cb132aeae2f7
Step 2/8 : COPY build.sh /bin/build.sh
 ---> 4b705965d849
Step 3/8 : ADD apollo-config.groovy /apollo/apollo-config.groovy
 ---> 43a3c9513e95
Step 4/8 : ENV WEBAPOLLO_VERSION 6189ff9e2973e1523ddcdbeee9d258c435c42a54
 ---> Running in ac59929f09d4
Removing intermediate container ac59929f09d4
 ---> 35be0d106992
Step 5/8 : RUN apk update && 	apk add --update tar && 	apk add curl ca-certificates bash nodejs git postgresql-client maven libpng 		make g++ zlib-dev expat-dev nodejs-npm sudo openssh-client perl && 	npm install -g bower && 	adduser -s /bin/bash -D -h /apollo apollo && 	curl -L https://github.com/GMOD/Apollo/archive/${WEBAPOLLO_VERSION}.tar.gz | 	tar xzf - --strip-components=1 -C /apollo && 	chown -R apollo:apollo /apollo && 	apk add openjdk8 openjdk8-jre && 	cp /usr/lib/jvm/java-1.8-openjdk/lib/tools.jar /usr/lib/jvm/java-1.8-openjdk/jre/lib/ext/tools.jar && 	sudo -u apollo /bin/build.sh && 	apk del curl bash nodejs git libpng make g++ nodejs-npm openjdk8 sudo
 ---> Running in addef1f810b6
fetch http://dl-cdn.alpinelinux.org/alpine/v3.8/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.8/community/x86_64/APKINDEX.tar.gz
v3.8.0-28-g923d74cddf [http://dl-cdn.alpinelinux.org/alpine/v3.8/main]
v3.8.0-28-g923d74cddf [http://dl-cdn.alpinelinux.org/alpine/v3.8/community]
OK: 9539 distinct packages available
(1/1) Installing tar (1.30-r0)
Executing busybox-1.28.4-r0.trigger
OK: 94 MiB in 63 packages
(1/38) Installing nghttp2-libs (1.32.0-r0)
(2/38) Installing libssh2 (1.8.0-r3)
(3/38) Installing libcurl (7.61.0-r0)
(4/38) Installing curl (7.61.0-r0)
(5/38) Installing expat (2.2.5-r0)
(6/38) Installing pkgconf (1.5.1-r0)
(7/38) Installing expat-dev (2.2.5-r0)
(8/38) Installing binutils (2.30-r5)
(9/38) Installing gmp (6.1.2-r1)
(10/38) Installing isl (0.18-r0)
(11/38) Installing libgomp (6.4.0-r8)
(12/38) Installing libatomic (6.4.0-r8)
(13/38) Installing mpfr3 (3.1.5-r1)
(14/38) Installing mpc1 (1.0.3-r1)
(15/38) Installing gcc (6.4.0-r8)
(16/38) Installing musl-dev (1.1.19-r10)
(17/38) Installing libc-dev (0.7.1-r0)
(18/38) Installing g++ (6.4.0-r8)
(19/38) Installing pcre2 (10.31-r0)
(20/38) Installing git (2.18.0-r0)
(21/38) Installing make (4.2.1-r2)
(22/38) Installing maven (3.5.4-r1)
(23/38) Installing c-ares (1.14.0-r0)
(24/38) Installing http-parser (2.8.1-r0)
(25/38) Installing libuv (1.20.2-r0)
(26/38) Installing nodejs (8.11.3-r1)
(27/38) Installing npm (8.11.3-r1)
(28/38) Installing openssh-keygen (7.7_p1-r2)
(29/38) Installing openssh-client (7.7_p1-r2)
(30/38) Installing perl (5.26.2-r1)
(31/38) Installing libedit (20170329.3.1-r3)
(32/38) Installing db (5.3.28-r0)
(33/38) Installing libsasl (2.1.26-r13)
(34/38) Installing libldap (2.4.46-r0)
(35/38) Installing libpq (10.4-r0)
(36/38) Installing postgresql-client (10.4-r0)
(37/38) Installing sudo (1.8.23-r2)
(38/38) Installing zlib-dev (1.2.11-r1)
Executing busybox-1.28.4-r0.trigger
OK: 370 MiB in 101 packages
npm WARN deprecated [email protected]: We don't recommend using Bower for new projects. Please consider Yarn and Webpack or Parcel. You can read how to migrate legacy project here: https://bower.io/blog/2017/how-to-migrate-away-from-bower/
/usr/bin/bower -> /usr/lib/node_modules/bower/bin/bower
+ [email protected]
added 1 package in 4.418s
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   153    0   153    0     0    187      0 --:--:-- --:--:-- --:--:--   187
100 84.3M    0 84.3M    0     0  4823k      0 --:--:--  0:00:17 --:--:-- 5970k
(1/1) Installing openjdk8 (8.171.11-r0)
Executing java-common-0.1-r0.trigger
OK: 389 MiB in 102 packages
+ export JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk/jre
+ JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk/jre
+ cd /apollo/
+ ./apollo deploy
Grails not found using grailsw
Gradle not found using gradlew
Node Version: 8
Npm Version: 5
javac 1.8.0_171 found
javac installed
JDK 1.8 found: javac 1.8.0_171
Downloading https://services.gradle.org/distributions/gradle-2.11-all.zip
...
Unzipping /apollo/.gradle/wrapper/dists/gradle-2.11-all/ace7yl0a7udokebb27mt9s3qr/gradle-2.11-all.zip to /apollo/.gradle/wrapper/dists/gradle-2.11-all/ace7yl0a7udokebb27mt9s3qr
Set executable permissions for: /apollo/.gradle/wrapper/dists/gradle-2.11-all/ace7yl0a7udokebb27mt9s3qr/gradle-2.11/bin/gradle
Final JBrowse settings [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]
Copying apollo plugin
Handling JBrowse release [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Handling JBrowse [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Setting up JBrowse... 
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
Installing JBrowse [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Cloning: https://github.com/GMOD/jbrowse into jbrowse-download
Cloning repo with https://github.com/GMOD/jbrowse,jbrowse-download,tags/9d765aecaee02a41844fed11a241fdb4c35fc9f8
Final github URL: GMOD/jbrowse#9d765aecaee02a41844fed11a241fdb4c35fc9f8
Using npm to install: GMOD/jbrowse#9d765aecaee02a41844fed11a241fdb4c35fc9f8
npm WARN deprecated [email protected]: Unmaintained namespace. Please use the file-saver package: https://www.npmjs.com/package/file-saver
npm notice created a lockfile as package-lock.json. You should commit this file.
+ [email protected]
added 86 packages in 55.924s
Moving JBrowse into position GMOD/jbrowse#9d765aecaee02a41844fed11a241fdb4c35fc9f8
:installJBrowse FAILED

FAILURE: Build failed with an exception.

* Where:
Build file '/apollo/build.gradle' line: 321

* What went wrong:
Execution failed for task ':installJBrowseScript'.
> A problem occurred starting process 'command './setup.sh''

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

BUILD FAILED

What did I miss?

Thank you in advance,

Michal