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install_dependencies.sh
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install_dependencies.sh
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#!/bin/bash
# Stop on error
set -e
## conda environment name
ENV_NAME=bds_atac
ENV_NAME_PY3=bds_atac_py3
## install wiggler or not
INSTALL_WIGGLER_AND_MCR=0
INSTALL_GEM=0
INSTALL_PEAKSEQ=0
## install packages from official channels (bioconda and r)
conda create -n ${ENV_NAME} --file requirements.txt -y -c defaults -c bioconda -c r -c bcbio -c daler -c asmeurer
conda create -n ${ENV_NAME_PY3} --file requirements_py3.txt -y -c defaults -c bioconda -c r -c bcbio -c daler -c asmeurer
### bash function definition
function add_to_activate {
if [[ ! -f $CONDA_INIT ]]; then
echo > $CONDA_INIT
fi
for i in "${CONTENTS[@]}"; do
if [[ $(grep "$i" "$CONDA_INIT" | wc -l ) == 0 ]]; then
echo $i >> "$CONDA_INIT"
fi
done
}
## install useful tools for BigDataScript
mkdir -p $HOME/.bds
cp -f ./utils/bds_scr ./utils/bds_scr_5min ./utils/kill_scr bds.config $HOME/.bds/
cp -rf ./utils/clusterGeneric/ $HOME/.bds/
## install additional packages
source activate ${ENV_NAME}
conda uninstall graphviz -y # graphviz in bioconda has segmentation fault bug
conda install graphviz -c anaconda -y
conda install ucsc-bedgraphtobigwig -c bioconda -y
conda install ucsc-bedtobigbed -c bioconda -y
CONDA_BIN=$(dirname $(which activate))
CONDA_EXTRA="$CONDA_BIN/../extra"
CONDA_ACTIVATE_D="$CONDA_BIN/../etc/conda/activate.d"
CONDA_INIT="$CONDA_ACTIVATE_D/init.sh"
CONDA_LIB="$CONDA_BIN/../lib"
if [[ $(find $CONDA_LIB -name '*egg-info*' -not -perm -o+r | wc -l ) > 0 ]]; then
find $CONDA_LIB -name '*egg-info*' -not -perm -o+r -exec dirname {} \; | xargs chmod o+r -R
fi
mkdir -p $CONDA_EXTRA $CONDA_ACTIVATE_D
### install Anshul's phantompeakqualtool
cd $CONDA_EXTRA
git clone https://github.com/kundajelab/phantompeakqualtools
chmod 755 -R phantompeakqualtools
CONTENTS=("export PATH=$CONDA_EXTRA/phantompeakqualtools:\$PATH")
add_to_activate
### disable locally installed python package lookup
CONTENTS=("export PYTHONNOUSERSITE=True")
add_to_activate
CONTENTS=("export PYTHONPATH=$CONDA_LIB/python2.7/site-packages:\$PYTHONPATH")
add_to_activate
if [[ ${INSTALL_WIGGLER_AND_MCR} == 1 ]]; then
conda install -y -c conda-forge bc
### install Wiggler (for generating signal tracks)
cd $CONDA_EXTRA
wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/align2rawsignal/align2rawsignal.2.0.tgz -N --no-check-certificate
tar zxvf align2rawsignal.2.0.tgz
rm -f align2rawsignal.2.0.tgz
CONTENTS=("export PATH=\$PATH:$CONDA_EXTRA/align2rawsignal/bin")
add_to_activate
### install MCR (560MB)
cd $CONDA_EXTRA
wget http://mitra.stanford.edu/kundaje/software/MCR2010b.bin -N --no-check-certificate
#wget https://personal.broadinstitute.org/anshul/softwareRepo/MCR2010b.bin -N --no-check-certificate
chmod 755 MCR2010b.bin
echo '-P installLocation="'${CONDA_EXTRA}'/MATLAB_Compiler_Runtime"' > tmp.stdin
./MCR2010b.bin -silent -options "tmp.stdin"
rm -f tmp.stdin
rm -f MCR2010b.bin
CONTENTS=(
"MCRROOT=${CONDA_EXTRA}/MATLAB_Compiler_Runtime/v714"
"LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MCRROOT}/runtime/glnxa64"
"LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MCRROOT}/bin/glnxa64"
"MCRJRE=\${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64"
"LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MCRJRE}/native_threads"
"LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MCRJRE}/server"
"LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MCRJRE}"
"XAPPLRESDIR=\${MCRROOT}/X11/app-defaults"
"export LD_LIBRARY_PATH"
"export XAPPLRESDIR")
add_to_activate
fi
# install PeakSeq
if [[ ${INSTALL_PEAKSEQ} == 1 ]]; then
cd $CONDA_EXTRA
wget http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_1.31.zip -N --no-check-certificate
unzip PeakSeq_1.31.zip
rm -f PeakSeq_1.31.zip
cd PeakSeq
make
chmod 755 bin/PeakSeq
cd $CONDA_BIN
ln -s $CONDA_EXTRA/PeakSeq/bin/PeakSeq
fi
source deactivate
source activate ${ENV_NAME_PY3}
CONDA_BIN=$(dirname $(which activate))
CONDA_EXTRA="$CONDA_BIN/../extra"
CONDA_ACTIVATE_D="$CONDA_BIN/../etc/conda/activate.d"
CONDA_INIT="$CONDA_ACTIVATE_D/init.sh"
CONDA_LIB="$CONDA_BIN/../lib"
if [[ $(find $CONDA_LIB -name '*egg-info*' -not -perm -o+r | wc -l ) > 0 ]]; then
find $CONDA_LIB -name '*egg-info*' -not -perm -o+r -exec dirname {} \; | xargs chmod o+r -R
fi
mkdir -p $CONDA_EXTRA $CONDA_ACTIVATE_D
### uninstall IDR 2.0.3 and install the latest one
conda uninstall idr -y
cd $CONDA_EXTRA
git clone https://github.com/kundajelab/idr
cd idr
python3 setup.py install
cd $CONDA_EXTRA
rm -rf idr
### disable locally installed python package lookup
CONTENTS=("export PYTHONNOUSERSITE=True")
add_to_activate
CONTENTS=("export PYTHONPATH=$CONDA_LIB/python3.5/site-packages:\$PYTHONPATH")
add_to_activate
# install GEM
if [[ ${INSTALL_GEM} == 1 ]]; then
cd $CONDA_EXTRA
wget http://groups.csail.mit.edu/cgs/gem/download/gem.v3.0.tar.gz -N --no-check-certificate
tar zxvf gem.v3.0.tar.gz
rm -f gem.v3.0.tar.gz
cd gem
chmod 755 gem.jar
cd $CONDA_BIN
ln -s $CONDA_EXTRA/gem/gem.jar
fi
source deactivate
echo == Installing dependencies has been successfully done. ==