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kineticsTools_on_nci
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kineticsTools_on_nci
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#install kineticsTools
# load python modules
module load python/2.7.6
# install pbcore
mkdir -p /short/sd34/ap5514/myapps/pbcore
cd /short/sd34/ap5514/myapps/pbcore
export PYTHONPATH=/short/sd34/ap5514/myapps/pbcore/lib/python2.7/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/pbcore/bin:$PATH
mkdir -p $PATH
#install pip for pbcore because pip isn't bundled with python versions before 2.7.9
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --prefix=/short/sd34/ap5514/myapps/pbcore
pip install requests[security] --prefix /short/sd34/ap5514/myapps/pbcore
git clone https://github.com/PacificBiosciences/pbcore.git # makes a weird "bin:" folder
cd pbcore
python -m pip install -r requirements.txt --prefix /short/sd34/ap5514/myapps/pbcore
python setup.py install --prefix /short/sd34/ap5514/myapps/pbcore
pip install h5py --prefix /short/sd34/ap5514/myapps/pbcore --ignore-installed
#make pbcore module
cd ~/mymodules/
mkdir pbcore
cd pbcore/
vim 1.2.10
#paste this to make module
#%Module1.0#####################################################################
source /opt/Modules/extensions/extensions.tcl
proc ModulesHelp { } {
puts stderr "\tAdds pbcore bin directory to the path"
}
module-whatis "pbcore"
soft-prereq python/2.7.6
#set pbcoreversion 1.2.1 #no version yet
prepend-path PATH /short/sd34/ap5514/myapps/pbcore/
prepend-path PYTHONPATH /short/sd34/ap5514/myapps/pbcore/lib/python2.7/site-packages
---------------------------------------------------------------------------------------------------------------------------
#pbcommand installation
# install pbcommand
mkdir -p /short/sd34/ap5514/myapps/pbcommand
cd /short/sd34/ap5514/myapps/pbcommand
export PYTHONPATH=/short/sd34/ap5514/myapps/pbcommand/lib/python2.7/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/pbcommand/bin:$PATH # makes a weird "bin:" folder
mkdir -p $PATH
#install pip for pbcommand because pip isn't bundled with python versions before 2.7.9
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --prefix=/short/sd34/ap5514/myapps/pbcommand
pip install requests[security] --prefix /short/sd34/ap5514/myapps/pbcommand
git clone https://github.com/PacificBiosciences/pbcommand.git
cd pbcommand
python -m pip install -r REQUIREMENTS.txt --prefix /short/sd34/ap5514/myapps/pbcommand
pip install win_inet_pton --prefix /short/sd34/ap5514/myapps/pbcommand # error returned where this requirement was not installed
# kept getting similar errors during kineticsTools installation to keep installing a missing dependency
pip install Pysocks --prefix /short/sd34/ap5514/myapps/pbcommand
pip install sphinx-rtd-theme --prefix /short/sd34/ap5514/myapps/pbcommand
pip install sphinx --prefix /short/sd34/ap5514/myapps/pbcommand --ignore-installed
pip install pretend --prefix /short/sd34/ap5514/myapps/pbcommand --ignore-installed #stopped here because the dependency was installed, but the wrong version.
python setup.py install --prefix /short/sd34/ap5514/myapps/pbcommand
#make pbcommand module
cd ~/mymodules/
mkdir pbcommand
cd pbcommand/
vim 0.2.17
#paste this to make module
#%Module1.0#####################################################################
source /opt/Modules/extensions/extensions.tcl
proc ModulesHelp { } {
puts stderr "\tAdds pbcore bin directory to the path"
}
module-whatis "pbcore"
soft-prereq python/2.7.6
set pbcoreversion 0.2.17
prepend-path PATH /short/sd34/ap5514/myapps/pbcommand/
prepend-path PYTHONPATH /short/sd34/ap5514/myapps/pbcommand/lib/python2.7/site-packages
--------------------------------------------------------------------------------------------------------------------------
#load modules for kineticsTools
module load pbcore
module load pbcommand
# make and call directory to install kineticsTools
mkdir -p /short/sd34/ap5514/myapps/kineticsTools
cd /short/sd34/ap5514/myapps/kineticsTools
export PYTHONPATH=/short/sd34/ap5514/myapps/kineticsTools/lib/python2.7/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/kineticsTools/bin:$PATH
mkdir -p $PATH
#install pip for kineticsTools because pip isn't bundled with python versions before 2.7.9
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --prefix=/short/sd34/ap5514/myapps/kineticsTools
pip install requests[security] --prefix /short/sd34/ap5514/myapps/kineticsTools
# Install kineticsTools
git clone https://github.com/PacificBiosciences/kineticsTools.git
cd kineticsTools
python setup.py install --prefix /short/sd34/ap5514/myapps/kineticsTools
# Install python requirements
module load python/2.7.6
python -m pip install h5py --upgrade pip --prefix /short/sd34/ap5514/myapps/kineticsTools --ignore-installed
python -m pip install numpy --upgrade pip --prefix /short/sd34/ap5514/myapps/kineticsTools --ignore-installed
python -m pip install scipy --upgrade pip --prefix /short/sd34/ap5514/myapps/kineticsTools --ignore-installed
#make module
cd ~/mymodules/
mkdir kineticstools
cd kineticstools/
vim version
#paste this to make module
#%Module1.0#####################################################################
source /opt/Modules/extensions/extensions.tcl
proc ModulesHelp { } {
puts stderr "\tAdds kineticsTools bin directory to the path"
}
module-whatis "kineticstools"
soft-prereq python/2.7.6
soft-prereq pbcore
soft-prereq pbcommand
#set kineticsToolsversion 1.2.1 #no version yet
prepend-path PATH /short/sd34/ap5514/myapps/kineticsTools/
prepend-path PYTHONPATH /short/sd34/ap5514/myapps/kineticsTools/lib/python2.7/site-packages