Docker_build fix (#75)

* Docker_build fix

* fix dockerfile

Docker/bdg-sequila/Dockerfile

@@ -13,6 +13,8 @@ ARG BDG_VERSION={{COMPONENT_VERSION}}
 ####set variable used in all shell scritps for downloading jars
 ENV BGD_VERSION={{COMPONENT_VERSION}}
 
+
+
 RUN mkdir /tmp/bdg-toolset
 
 ###once the repo is public we can use git instead
@@ -29,7 +31,10 @@ COPY bin/bdg-sequilaR.sh /tmp/bdg-toolset/bdg-sequilaR
 
 #featureCounts scripts
 COPY bin/featureCounts.sh /tmp/bdg-toolset/featureCounts
-RUN wget https://zsibio.ii.pw.edu.pl/nexus/repository/maven-snapshots/org/biodatageeks/bdg-sequila_2.11/${BGD_VERSION}/bdg-sequila_2.11-${BGD_VERSION}-assembly.jar -O /tmp/bdg-toolset/bdg-sequila-assembly-${BGD_VERSION}.jar
+RUN bash -c " if [[ $BDG_VERSION =~ *SNAPSHOT ]]; then \
+    wget https://zsibio.ii.pw.edu.pl/nexus/repository/maven-snapshots/org/biodatageeks/bdg-sequila_2.11/${BGD_VERSION}/bdg-sequila_2.11-${BGD_VERSION}-assembly.jar -O /tmp/bdg-toolset/bdg-sequila-assembly-${BGD_VERSION}.jar ; \
+    else wget https://zsibio.ii.pw.edu.pl/nexus/repository/maven-releases/org/biodatageeks/bdg-sequila_2.11/${BGD_VERSION}/bdg-sequila_2.11-${BGD_VERSION}-assembly.jar -O /tmp/bdg-toolset/bdg-sequila-assembly-${BGD_VERSION}.jar ; \
+    fi"
 
 #copy test data
 COPY NA12878.slice.bam /tmp/NA12878.slice.bam

build.sbt

@@ -93,11 +93,11 @@ assemblyMergeStrategy in assembly := {
 }
 
 /* only for releasing assemblies*/
-//artifact in (Compile, assembly) := {
-//  val art = (artifact in (Compile, assembly)).value
-//  art.withClassifier(Some("assembly"))
-//}
-//addArtifact(artifact in (Compile, assembly), assembly)
+artifact in (Compile, assembly) := {
+  val art = (artifact in (Compile, assembly)).value
+  art.withClassifier(Some("assembly"))
+}
+addArtifact(artifact in (Compile, assembly), assembly)
 
 publishConfiguration := publishConfiguration.value.withOverwrite(true)
 

build.sh

@@ -31,8 +31,8 @@ do
     fi
   #fi
   echo "Building image ${image}..."
-  diffTs=`echo "$(date +%s) - $(git log -n 1 --pretty=format:%at ${dir})" | bc`
-  if [ $diffTs -lt $MAX_COMMIT_TS_DIFF ]; then
+  #diffTs=`echo "$(date +%s) - $(git log -n 1 --pretty=format:%at ${dir})" | bc`
+  #if [ $diffTs -lt $MAX_COMMIT_TS_DIFF ]; then
     cd $dir
     docker build  -t $image:$version .
     docker build  -t $image:latest .
@@ -50,6 +50,6 @@ do
     docker images $image | tail -n +5 | sed 's/ \{1,\}/:/g' | cut -f1,2 -d':' | xargs -i docker rmi {}
 
     cd ../..
-  fi
+  #fi
 
 done

build_docs.sh

@@ -7,7 +7,7 @@ echo Version is $version
 
 cd docs && ./docs.sh html
 
-if [[ $OSTYPE =~ *SNAPSHOT ]]; then
+if [[ $version =~ *SNAPSHOT ]]; then
     docker build -t zsi-bio/bdg-sequila-snap-doc .
     if [ $(docker ps | grep bdg-sequila-snap-doc | wc -l) -gt 0 ]; then docker stop bdg-sequila-snap-doc && docker rm bdg-sequila-snap-doc; fi
     docker run -v 80:81 -d --name bdg-sequila-snap-doc zsi-bio/bdg-sequila-snap-doc