{AH} use conda to download bcftools etc, closes
@@ -15,7 +15,7 @@ bash Miniconda3.sh -b
# Create a new conda environment with the target python version
~/miniconda3/bin/conda install conda-build -y
-~/miniconda3/bin/conda create -q -y --name testenv python=$CONDA_PY cython numpy nose psutil pip
+~/miniconda3/bin/conda create -q -y --name testenv python=$CONDA_PY cython numpy nose psutil pip samtools bcftools htslib
# activate testenv environment
source ~/miniconda3/bin/activate testenv
@@ -25,54 +25,10 @@ export PREFIX=~/miniconda3/
export CFLAGS="-I${PREFIX}/include -L${PREFIX}/lib"
export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
-# create a new folder to store external tools
-mkdir -p $WORKDIR/external-tools
-
-# install htslib
-cd $WORKDIR/external-tools
-curl --retry-delay 60 --retry 5 -L https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2 > htslib-1.3.1.tar.bz2
-tar xjvf htslib-1.3.1.tar.bz2
-cd htslib-1.3.1
-make
-PATH=$PATH:$WORKDIR/external-tools/htslib-1.3.1
-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$WORKDIR/external-tools/htslib-1.3.1
-
-# install samtools, compile against htslib
-cd $WORKDIR/external-tools
-curl --retry-delay 60 --retry 5 -L http://downloads.sourceforge.net/project/samtools/samtools/1.3.1/samtools-1.3.1.tar.bz2 > samtools-1.3.1.tar.bz2
-
-tar xjvf samtools-1.3.1.tar.bz2
-cd samtools-1.3.1
-./configure --with-htslib=../htslib-1.3.1
-make
-PATH=$PATH:$WORKDIR/external-tools/samtools-1.3.1
-
-echo "installed samtools"
samtools --version
-
-if [ $? != 0 ]; then
- exit 1
-fi
-
-# install bcftools
-cd $WORKDIR/external-tools
-curl --retry-delay 60 --retry 5 -L https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 > bcftools-1.3.1.tar.bz2
-
-tar xjf bcftools-1.3.1.tar.bz2
-cd bcftools-1.3.1
-./configure --with-htslib=../htslib-1.3.1
-make
-PATH=$PATH:$WORKDIR/external-tools/bcftools-1.3.1
-
-echo "installed bcftools"
+htslib --version
bcftools --version
-if [ $? != 0 ]; then
- exit 1
-fi
-
-popd
-
# Try building conda recipe first
~/miniconda3/bin/conda-build ci/conda-recipe/ --python=$CONDA_PY
