====== SALSA ======

A tool to scaffold long read assemblies with Hi-C data.

===== Information =====

  * Version: git-974589f3
  * Added: November, 2020
  * Link: https://github.com/marbl/SALSA

===== Usage =====

See which versions of salsa are available:
<code>$ module avail salsa</code>

Load one version into your environment and run it:
<code>$ module load salsa/git-974589f3
$ run_pipeline.py</code>

See the SALSA documentation for more information about running the pipeline: https://github.com/marbl/SALSA#how-to-run-the-code

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>