This is a wrap around for many of commonly used pipelines and supports submission through IBM LSF bsub command. If you want to add other batch submission systems, then you have edit the /bin/farmsub.sh file to support it.
This is primarily written in linux bash. Some of these may be incompatible with Mac bash and needless to say Windows is out of question. It requires you to install all the packages (some are given below) that it uses in its various sub commands.
The main config file in ~/$HOME/.pisan/conf If you provide a conf file with the commands it will overwrite options of pisan.conf
In the conf file you have to change the variable to point to the path where pisan is installed
mconf_installdir="$HOME/Software/pisan"
echo "PATH=$USER/Software/pisan/bin:$PATH" >> $HOME/.bashrc
pisan - Generates all the suite commands available
each command is a bash file in the bin folder.
All relevant tools should be added to your $PATH. The main ones are
- Rscript
- BASH
- BASH -> getopts
- samtools
- biobambam2
- anaconda python = create a python2.7 environment with name p27
- anaconda python = create a python3 environment with name p3
pisan sources the main and local config files. Local config files overwrite main config
It then reads in arguments from src/general_args.sh and functions from src/basic_functions.sh