testing something

broadinstitute · Jul 6, 2018 · 0f0958d · 0f0958d
1 parent 9e37c44
commit 0f0958d
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Showing 3 changed files with 11 additions and 1 deletion.
diff --git a/Dockerfile b/Dockerfile
@@ -35,7 +35,7 @@ RUN echo "source activate gatk" > /root/run_unit_tests.sh && \
     echo "export CP_DIR=/gatk/testClasses" /root/run_unit_tests.sh && \
     echo "ln -s /gatkCloneMountPoint/src/ /gatkCloneMountPoint/scripts/docker/src" >> /root/run_unit_tests.sh && \
     echo "ln -s /gatkCloneMountPoint/build/ /gatkCloneMountPoint/scripts/docker/build" >> /root/run_unit_tests.sh && \
-    echo "cd /gatk/ && /gatkCloneMountPoint/gradlew -b /gatkCloneMountPoint/dockertest.gradle testOnPackagedReleaseJar jacocoTestReportOnPackagedReleaseJar -a -p /gatkCloneMountPoint" >> /root/run_unit_tests.sh
+    echo "cd /gatk/ && /gatkCloneMountPoint/gradlew -b /gatkCloneMountPoint/dockertest.gradle testOnPackagedReleaseJar -Dtest.single=PlotModeledSegmentsIntegrationTest jacocoTestReportOnPackagedReleaseJar -a -p /gatkCloneMountPoint" >> /root/run_unit_tests.sh
 
 WORKDIR /root
 RUN cp -r /root/run_unit_tests.sh /gatk

diff --git a/scripts/docker/dockertest.gradle b/scripts/docker/dockertest.gradle
@@ -12,6 +12,14 @@ plugins {
     id "jacoco"
 }
 
+repositories {
+    mavenCentral()
+    jcenter()
+    maven {
+        url "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot/" //for htsjdk snapshots
+    }
+    mavenLocal()
+}
 
 //============================================================================================================================
 // WARNING

diff --git a/...in/resources/org/broadinstitute/hellbender/tools/copynumber/plotting/CNVPlottingLibrary.R b/...in/resources/org/broadinstitute/hellbender/tools/copynumber/plotting/CNVPlottingLibrary.R
@@ -3,6 +3,8 @@ ReadTSV = function(tsv_file) {
     # however, the standard 'fread("grep ...")' causes issues with the default Docker container, so we use a temporary file.
     # See https://github.com/broadinstitute/gatk/issues/4140.
     temp_file = tempfile()
+    write(tsv_file, stderr())
+    write(temp_file, stderr())
     system(sprintf("grep -v ^@ %s > %s", tsv_file, temp_file))
     return(suppressWarnings(fread(temp_file, sep="\t", stringsAsFactors=FALSE, header=TRUE, check.names=FALSE, data.table=FALSE, showProgress=FALSE, verbose=FALSE)))
 }