smrtpipe_on_nci

#installation for smrtpipe on nci

mkdir -p /short/sd34/ap5514/myapps/smrtlink/5.1.0/smrtcmds/bin/graphviz/2.40.1
export PYTHONPATH=/short/sd34/ap5514/myapps/smrtlink/5.1.0/smrtcmds/bin/graphviz/2.40.1/lib/python2.7/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/smrtlink/5.1.0/smrtcmds/bin/graphviz:$PATH
cd $PATH

#install graphviz requirement, so dot is added to the smrtcmds directory in smrtlink
wget https://graphviz.gitlab.io/pub/graphviz/stable/SOURCES/graphviz.tar.gz
wget https://graphviz.gitlab.io/pub/graphviz/stable/SOURCES/graphviz.tar.gz.md5

#check if md5sum are the same
md5sum -c graphviz.tar.gz.md5

#install smrtpipe
cd /short/sd34/ap5514/myapps/smrtlink/5.1.0/smrtcmds/bin
export PATH=/short/sd34/ap5514/myapps/smrtlink/5.1.0/smrtcmds/bin:$PATH
export PYTHONPATH=/short/sd34/ap5514/myapps/smrtlink/5.1.0/smrtcmds/bin
git clone https://github.com/PacificBiosciences/pbsmrtpipe.git
cd pbsmrtpipe
# this will install pbcore and pbcommand
pip install -r PB_REQUIREMENTS.txt # this will install pbcommand and pbcore from master on github
pip install -r REQUIREMENTS.txt # will install from pypi
pip install .
pbsmrtpipe --help

python -m pip --prefix