Skip to content

Instantly share code, notes, and snippets.

@chapmanb

chapmanb/bcbio_vm_install.sh

Created January 29, 2019 15:54
Show Gist options
  • Save chapmanb/165576205be37533871a0efa7e8aedc4 to your computer and use it in GitHub Desktop.
Save chapmanb/165576205be37533871a0efa7e8aedc4 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment