A tool to scaffold long read assemblies with Hi-C data.
See which versions of salsa are available:
$ module avail salsa
Load one version into your environment and run it:
$ module load salsa/git-974589f3 $ run_pipeline.py
See the SALSA documentation for more information about running the pipeline: https://github.com/marbl/SALSA#how-to-run-the-code
Notes from the sysadmin during installation:
$ cd /tmp $ git clone https://github.com/marbl/SALSA.git $ cd SALSA $ make $ chmod -x *.cpp *.h $ chmod +x run_pipeline.py # add python2 shebangs to all Python scripts $ sudo mkdir -p /export/apps/salsa/git-974589f3 $ sudo chown aorth /export/apps/salsa/git-974589f3 $ chmod +x convert.sh # update the JUICER_JAR variable in convert.sh (not sure which version we need???) $ cp * /export/apps/salsa/git-974589f3 $ python2 -m virtualenv /export/apps/salsa/git-974589f3/venv $ source /export/apps/salsa/git-974589f3/venv/bin/activate $ pip install --upgrade pip setuptools $ pip install networkx==1.11 $ sudo chown -R root:root /export/apps/salsa/git-974589f3