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SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.



See versions of sepp which are available:

$ module avail sepp

Load one version into your environment and run it:

$ module load sepp/4.5.1
$ -h

The general command for running SEPP is: -t <tree_file> -a <alignment_file> -f <fragment_file> -r <raxml_info_file> -A <alignment_set_size> -P <placement_set_size>

Note: please use the "-x" or "–cpu" options to set the number of CPUs for your SEPP run. This number should match the number of CPUs requested in your SBATCH allocation.


Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/sepp/4.5.1
$ sudo chown aorth:aorth /export/apps/sepp/4.5.1
$ git clone -b 4.5.1 /export/apps/sepp/4.5.1
$ cd /export/apps/sepp/4.5.1
$ python3 -m venv venv
$ source venv/bin/activate
$ pip install --upgrade pip setuptools
$ python config -c
$ python install
$ sed -i 's?/usr/bin/env python?/usr/bin/env python3?' run_*.py
$ sudo chown -R root:root /export/apps/sepp/4.5.1

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: 2021/12/28 13:49 by aorth