====== 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: 4.5.1
  * Added: May, 2020
  * Updated: December, 2021
  * Link: https://github.com/smirarab/sepp

===== Usage =====

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

Load one version into your environment and run it:

<code>$ module load sepp/4.5.1
$ run_sepp.py -h</code>

The general command for running SEPP is:

<code>run_sepp.py -t <tree_file> -a <alignment_file> -f <fragment_file> -r <raxml_info_file> -A <alignment_set_size> -P <placement_set_size></code>

**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. 

===== Installation ======
Notes from the sysadmin during installation:

<code>$ sudo mkdir -p /export/apps/sepp/4.5.1
$ sudo chown aorth:aorth /export/apps/sepp/4.5.1
$ git clone https://github.com/smirarab/sepp.git -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 setup.py config -c
$ python setup.py install
$ sed -i 's?/usr/bin/env python?/usr/bin/env python3?' run_*.py split_sequences.py
$ sudo chown -R root:root /export/apps/sepp/4.5.1</code>

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.