salsa-software
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Table of Contents
SALSA
A tool to scaffold long read assemblies with Hi-C data.
Information
- Version: git-974589f3
- Added: November, 2020
Usage
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
Installation
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 $ 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
salsa-software.1605171271.txt.gz · Last modified: 2020/11/12 08:54 by aorth