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chapmanb/bcbio_vm_install.sh

Created January 29, 2019 15:54
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bcbio_vm_install.sh
#!/bin/bash
set -eu -o pipefail
export TARGETDIR=`pwd`/anaconda
export BINDIR=`pwd`
wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b -p $TARGETDIR
$TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen
$TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm
mkdir -p $BINDIR/bin
ln -s $TARGETDIR/bin/bcbio_vm.py $BINDIR/bcbio_vm.py
ln -s $TARGETDIR/bin/conda $BINDIR/bcbiovm_conda
ln -s $TARGETDIR/bin/python $BINDIR/bcbiovm_python
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