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 $ run_sepp.py -h
The general command for running SEPP is:
run_sepp.py -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 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
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.