From 765cb75beb4db735bec1cd9ef0568d6d7f581842 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marek=20Wiewi=C3=B3rka?= <marek.wiewiorka@gmail.com>
Date: Thu, 26 Apr 2018 17:49:55 +0200
Subject: [PATCH] Docker_build fix (#75)

* Docker_build fix

* fix dockerfile
---
 Docker/bdg-sequila/Dockerfile |  7 ++++++-
 build.sbt                     | 10 +++++-----
 build.sh                      |  6 +++---
 build_docs.sh                 |  2 +-
 4 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/Docker/bdg-sequila/Dockerfile b/Docker/bdg-sequila/Dockerfile
index 9feb7dfd..851e3d89 100644
--- a/Docker/bdg-sequila/Dockerfile
+++ b/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
diff --git a/build.sbt b/build.sbt
index ea6a8e1e..4d5cafef 100644
--- a/build.sbt
+++ b/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)
 
diff --git a/build.sh b/build.sh
index dbdff4df..b799f8fa 100755
--- a/build.sh
+++ b/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
diff --git a/build_docs.sh b/build_docs.sh
index c18c65f8..08956ecb 100755
--- a/build_docs.sh
+++ b/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