User Tools

Site Tools


sepp-software

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

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.txt · Last modified: 2020/05/12 08:13 by aorth