broadinstitute · dpark01 · Sep 10, 2019 · Sep 10, 2019 · Sep 10, 2019 · Sep 10, 2019
diff --git a/.travis.yml b/.travis.yml
@@ -8,10 +8,8 @@ env:
   global:
   - CACHE_DIR="$HOME/misc_cache"
   - MINICONDA_DIR="$HOME/miniconda"
-  - PIP_DIR="$HOME/virtualenv"
   - GATK_PATH="$CACHE_DIR"
   - PYTHONIOENCODING=UTF8
-  - PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov kmer_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils"
 
   - DOCKER_REGISTRY="quay.io"
   - DOCKER_REPO_PROD="quay.io/broadinstitute/micro-readqc"
@@ -85,6 +83,7 @@ jobs:
       stage: test
       env:
         - TRAVIS_JOB=test_py36_in_docker
+        - PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov read_utils --cov reports --cov tools --cov util --cov file_utils"
       install:
         - DOCKER_TAG=`travis/list-docker-tags.sh | tail -1`
         - docker pull $DOCKER_TAG

diff --git a/test/input/TestDepleteHuman/aligned-expected/test-reads.blastn.bam b/test/input/TestDepleteHuman/aligned-expected/test-reads.blastn.bam
diff --git a/test/input/TestDepleteHuman/aligned-expected/test-reads.bmtagger.bam b/test/input/TestDepleteHuman/aligned-expected/test-reads.bmtagger.bam
diff --git a/test/input/TestDepleteHuman/aligned-expected/test-reads.bwa.bam b/test/input/TestDepleteHuman/aligned-expected/test-reads.bwa.bam
diff --git a/test/input/TestDepleteHuman/aligned-expected/test-reads.revert.bam b/test/input/TestDepleteHuman/aligned-expected/test-reads.revert.bam
diff --git a/test/input/TestDepleteHuman/aligned-expected/test-reads.rmdup.bam b/test/input/TestDepleteHuman/aligned-expected/test-reads.rmdup.bam
diff --git a/test/input/TestDepleteHuman/aligned-expected/test-reads.taxfilt.imperfect.bam b/test/input/TestDepleteHuman/aligned-expected/test-reads.taxfilt.imperfect.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.blastn.bam b/test/input/TestDepleteHuman/expected/test-reads.blastn.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.bmtagger.bam b/test/input/TestDepleteHuman/expected/test-reads.bmtagger.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.bwa.bam b/test/input/TestDepleteHuman/expected/test-reads.bwa.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.revert.bam b/test/input/TestDepleteHuman/expected/test-reads.revert.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.rmdup.bam b/test/input/TestDepleteHuman/expected/test-reads.rmdup.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.taxfilt.bam b/test/input/TestDepleteHuman/expected/test-reads.taxfilt.bam
diff --git a/test/input/TestDepleteHuman/expected/test-reads.taxfilt.imperfect.bam b/test/input/TestDepleteHuman/expected/test-reads.taxfilt.imperfect.bam
diff --git a/test/input/TestDepleteHuman/partial_pan-viral-9seqs-with-human-random-subset.fasta b/test/input/TestDepleteHuman/partial_pan-viral-9seqs-with-human-random-subset.fasta
diff --git a/test/input/TestDepleteHuman/test-reads-aligned.bam b/test/input/TestDepleteHuman/test-reads-aligned.bam
diff --git a/test/input/TestDepleteHuman/test-reads-human.bam b/test/input/TestDepleteHuman/test-reads-human.bam
diff --git a/test/input/TestDepleteHuman/test-reads.bam b/test/input/TestDepleteHuman/test-reads.bam
diff --git a/travis/before_install.sh b/travis/before_install.sh
@@ -14,7 +14,7 @@ if [ -z "$TRAVIS_TAG" ]; then
 
     # Report how big things are
     echo "Docker cache space usage:"
-    du -hs $MINICONDA_DIR $PIP_DIR $CACHE_DIR/*
+    du -hs $MINICONDA_DIR $CACHE_DIR/*
 else
     echo "Travis docker cache disabled for tools/build on tag: $TRAVIS_TAG"
 fi