Purdue University

Commands

• proteinortho
• proteinortho2html.pl
• proteinortho2tree.pl
• proteinortho2xml.pl
• proteinortho6.pl
• proteinortho_cleanupblastgraph
• proteinortho_clustering
• proteinortho_compareProteinorthoGraphs.pl
• proteinortho_do_mcl.pl
• proteinortho_extract_from_graph.pl
• proteinortho_ffadj_mcs.py
• proteinortho_formatUsearch.pl
• proteinortho_grab_proteins.pl
• proteinortho_graphMinusRemovegraph
• proteinortho_history.pl
• proteinortho_singletons.pl
• proteinortho_summary.pl
• proteinortho_treeBuilderCore

Module

You can load the modules by:

module load biocontainers
module load proteinortho

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Proteinortho on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=proteinortho
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers proteinortho

proteinortho6.pl test/C.faa test/E.faa test/L.faa test/M.faa