Merge eb8711f into 40f724a

reports.py

@@ -582,10 +582,6 @@ def plot_coverage(
     ''' 
         Generate a coverage plot from an aligned bam file
     '''
-
-    # TODO: remove this:
-    #coverage_tsv_file = "/Users/tomkinsc/Downloads/plottest/test_multisegment.tsv"
-
     samtools = tools.samtools.SamtoolsTool()
 
     # check if in_bam is aligned, if not raise an error

travis/install-conda.sh

@@ -39,7 +39,7 @@ else # if it does not exist, we need to install miniconda
         export PATH="$MINICONDA_DIR/bin:$PATH"
     fi
     hash -r
-    conda config --set always_yes yes --set changeps1 no
+    conda config --set always_yes yes --set changeps1 no --set remote_max_retries 6
     conda config --add channels defaults
     conda config --add channels bioconda
     conda config --add channels conda-forge
@@ -49,4 +49,6 @@ else # if it does not exist, we need to install miniconda
     conda install --quiet -y openjdk==8.0.112
 fi
 
+# update certs
+conda update --quiet -y openssl pyopenssl ca-certificates certifi
 conda info -a # for debugging

travis/install-tools.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-set -e -o pipefail
+set -e -o pipefail #exit on error or within pipes
 
 CONDA_CHANNEL_STRING="--override-channels -c broad-viral -c conda-forge -c bioconda -c defaults"
 CONDA_ENV="$(pwd)/tools/conda-tools/default"
@@ -13,15 +13,31 @@ export CONDA_ENVS_PATH=tools/conda-cache:tools/conda-tools/default
 PYVER=`echo $TRAVIS_PYTHON_VERSION | cut -c 1`
 
 if [ ! -d $CONDA_ENV ]; then
-	conda create -y -m --quiet -p $CONDA_ENV python="$TRAVIS_PYTHON_VERSION"
+    conda create -y -m --quiet -p $CONDA_ENV python="$TRAVIS_PYTHON_VERSION" || exit $?
 fi
 
+# commented out custom retry logic for now
+# until we establish the built-in conda retry logic
+# works as intended when we retry more than the default
+# 3 times
+# remote_max_retries is set in install-conda.sh
+#set +e # disable exit on error
+#RETRIES=0
+#RETRY_LIMIT=3
+#until #conda...
 conda install -y --quiet \
-	$CONDA_CHANNEL_STRING \
-	--file requirements-conda.txt \
-	--file requirements-conda-tests.txt \
-	--file requirements-py$PYVER.txt \
-	-p $CONDA_ENV
+    $CONDA_CHANNEL_STRING \
+    --file requirements-conda.txt \
+    --file requirements-conda-tests.txt \
+    --file requirements-py$PYVER.txt \
+    -p $CONDA_ENV #; do
+#        let RETRIES++
+#        if [ "$RETRIES" -gt "$RETRY_LIMIT" ]; then
+#            break
+#        fi
+#        echo "Conda install failed, likely due to transient server errors. Retrying (${RETRIES}/${RETRY_LIMIT})..."
+#done
+#set -e #(re)enable exit on error
 
 conda clean --all --yes # clean temp/cache files to reduce Travis cache size