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mcaller_on_nci
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### need to reinstall everything for python 2.7, mCaller doesn't run on python3
# install biopython
module load python/2.7.5
mkdir -p /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc
export PYTHONPATH=/short/sd34/ap5514/myapps/nanopolish/0.9.0_mc/lib/python2.7/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/nanopolish/0.9.0_mc/bin:$PATH #maybe change path to include pip
#install pip for nanopolish
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --prefix=/short/sd34/ap5514/myapps/nanopolish/0.9.0_mc
pip install requests[security] --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc #error installing pycpurser
pip install biopython --upgrade pip --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc --ignore-installed
# install pysam
pip install pysam --upgrade pip --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc --ignore-installed
#load all the required modules incluing gcc-4.8+ and eigen and hdf5 and hts
module load gcc/4.9.0
module load hdf5/1.8.14p #--enable-threadsafe
module load eigen/3.2.8
module load htslib/1.4
#install nanopolish
mkdir /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc/bin/nanopolish
cd /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc/bin/nanopolish # make sure nanopolish files are sent to the right folder
git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
make EIGEN=noinstall HTS=noinstall # HDF5=noinstall flag was not used because NCI didn't have threadsafe hdf5 installed
# used threadsafe hdf5 installed by nanopolish
# many "warning: will never be executed" messages during "make" for installing nanopolish prereqs
"cannot optimise loop, the loop counter may overflow"
# write nanopolish module
cd ~/mymodules
mkdir nanopolish
cd nanopolish
vim 0.9.0_mc
#paste this
#%Module1.0#####################################################################
source /opt/Modules/extensions/extensions.tcl
proc ModulesHelp { } {
puts stderr "\tAdds nanopolish_mc bin directory to the path"
}
module-whatis "nanopolish_mc"
soft-prereq python/2.7.5
soft-prereq hdf5/1.8.14
soft-prereq eigen/3.2.8
soft-prereq htslib/1.4
soft-prereq minimap2
set nanopolish_mcversion 0.9.0
prepend-path PATH /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc/bin/nanopolish
prepend-path PYTHONPATH /short/sd34/ap5514/myapps/nanopolish/0.9.0_mc/lib/python2.7/site-packages
#install mcaller
# load python modules
module load python/2.7.5
module load python/2.7.5-matplotlib
# make and call directory to install mcaller
mkdir -p /short/sd34/ap5514/myapps/mcaller2/
cd /short/sd34/ap5514/myapps/mcaller2/
export PYTHONPATH=/short/sd34/ap5514/myapps/mcaller2/lib/python2.7/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/mcaller2/bin:$PATH
mkdir -p $PATH
# Install
git clone git@github.com:AnjuniPeiris/mCaller.git
# remove excess files
rm -rf bioRxiv/
rm -rf testdata
#install pip for mcaller
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --prefix=/short/sd34/ap5514/myapps/mcaller2
pip install requests[security] --prefix /short/sd34/ap5514/myapps/mcaller2 #error installing pycpurser
# Install python requirements
module load python/2.7.5
python -m pip install scikit-learn --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed
python -m pip install h5py --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed
#python -m pip install matplotlib --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed
python -m pip install seaborn --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed # DID NOT WORK
python -m pip install numpy --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed
python -m pip install pysam --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed
python -m pip install scipy --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed
python -m pip install pandas --upgrade pip --prefix /short/sd34/ap5514/myapps/mcaller2/ --ignore-installed #DID NOT WORK
#paste this to make module
#%Module1.0#####################################################################
source /opt/Modules/extensions/extensions.tcl
proc ModulesHelp { } {
puts stderr "\tAdds mCaller bin directory to the path"
}
module-whatis "mcaller2"
soft-prereq python/2.7.5
soft-prereq python/2.7.5-matplotlib
soft-prereq minimap2
soft-prereq nanopolish
#set mcallerversion 1.2.1 #no version yet
prepend-path PATH /short/sd34/ap5514/myapps/mcaller/mCaller/mCaller.py
prepend-path PATH /short/sd34/ap5514/myapps/mcaller/mCaller/make_bed.py
prepend-path PYTHONPATH /short/sd34/ap5514/myapps/mcaller/lib/python2.7/site-packages