more build verbosity and update upstream core to 2.0.5

.travis.yml

@@ -44,10 +44,11 @@ jobs:
         - set -e
         - if [ -f "$CACHE_DIR/old-docker-tag.txt" ]; then OLD_DOCKER_TAG=$(cat $CACHE_DIR/old-docker-tag.txt); else OLD_DOCKER_TAG=$DOCKER_REPO_PROD; fi; echo "old docker tag = $OLD_DOCKER_TAG"
         - _CACHE_FROM="--cache-from $OLD_DOCKER_TAG"; docker pull $OLD_DOCKER_TAG || _CACHE_FROM=""
+        - git describe --tags --always | tee VERSION
         - docker build -t local/build-container:build $_CACHE_FROM .
         - travis/deploy-docker.sh
       before_cache:
-        - travis/list-docker-tags.sh | tail -1 > $CACHE_DIR/old-docker-tag.txt
+        - travis/list-docker-tags.sh | tail -1 | tee $CACHE_DIR/old-docker-tag.txt
 
     - language: python
       stage: test
@@ -56,13 +57,14 @@ jobs:
         - PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov assembly"
       install:
         - DOCKER_TAG=`travis/list-docker-tags.sh | tail -1`
+        - echo "pulling $DOCKER_TAG"
         - docker pull $DOCKER_TAG
-        - pip install coveralls==1.1
         - mkdir coverage
       script:
         - docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/test:/opt/viral-ngs/source/test -v `pwd`/coverage:/coverage --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; pytest test/unit; cp .coverage /coverage'
       after_success:
         - mv coverage/.coverage .
+        - pip install coveralls==1.1
         - coveralls
 
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.0.3
+FROM quay.io/broadinstitute/viral-core:2.0.5
 
 LABEL maintainer "viral-ngs@broadinstitute.org"