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Fix pip 10 errors and directory error #1

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Fix pip 10 errors and directory error #1

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6 changes: 3 additions & 3 deletions nanopolish_on_NCI
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@ mkdir -p /short/sd34/ap5514/myapps/nanopolish/0.9.0
export PYTHONPATH=/short/sd34/ap5514/myapps/nanopolish/0.9.0/lib/python3.6/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/nanopolish/0.9.0/bin:$PATH
pip3 install biopython --upgrade pip --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0 --ignore-installed
python3 -m pip install biopython --upgrade pip --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0 --ignore-installed

# install pysam
pip3 install pysam --upgrade pip --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0 --ignore-installed
python3 -m pip install pysam --upgrade pip --prefix /short/sd34/ap5514/myapps/nanopolish/0.9.0 --ignore-installed

#load all the required modules incluing gcc-4.8+ and eigen and hdf5 and hts
module load gcc/4.9.0
Expand All @@ -16,7 +16,7 @@ module load eigen/3.2.8
module load htslib/1.4

#install nanopolish
cd /short/sd34/ap5514/myapps/nanopolish/0.9.0/bin/nanopolish # make sure nanopolish files are sent to the right folder
cd /short/sd34/ap5514/myapps/nanopolish/0.9.0/bin/ # 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
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