sepp-software
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Table of Contents
sepp
SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
Information
- Version: 4.3.8
- Added: May, 2020
Usage
See versions of sepp which are available:
$ module avail sepp
Load one version into your environment and run it:
$ module load sepp/4.3.8 $ run_sepp.py
Installation
Notes from the sysadmin during installation:
$ sudo mkdir -p /export/apps/sepp/4.3.8 $ sudo chown aorth /export/apps/sepp/4.3.8 $ git clone https://github.com/smirarab/sepp.git -b 4.3.8 /export/apps/sepp/4.3.8 $ cd /export/apps/sepp/4.3.8 $ python3 -m venv venv $ source venv/bin/activate $ python setup.py config -c $ python setup.py install $ sed -i 's?/usr/bin/env python?/usr/bin/env python3?' run_sepp.py $ sudo chown -R root:root /export/apps/sepp/4.3.8
Sepp's setup script wants to write the main.config
file in the user's home directory or the source directory, so we need to clone the git repository to /export/apps
where we intend to install it and then use the local (-c
) config option.
sepp-software.1589271230.txt.gz · Last modified: 2020/05/12 08:13 by aorth