Purdue University

Commands

• aa_comp_calculator.py
• aa_recoder.py
• apply_to_db.py
• astral_runner.py
• backup_restoration.py
• bipartition_examiner.py
• build_database.py
• config.py
• edirect.py
• explore_database.py
• fast_site_remover.py
• fast_taxa_remover.py
• fisher.py
• forest.py
• genetic_code_examiner.py
• gfmix_runner.py
• heterotachy.py
• informant.py
• install_deps.py
• jp.py
• mammal_modeler.py
• matrix_constructor.py
• prep_final_dataset.py
• purge.py
• random_resampler.py
• rst2html.py
• rst2html4.py
• rst2html5.py
• rst2latex.py
• rst2man.py
• rst2odt.py
• rst2odt_prepstyles.py
• rst2pseudoxml.py
• rst2s5.py
• rst2xetex.py
• rst2xml.py
• rstpep2html.py
• rtc_binner.py
• runxlrd.py
• select_orthologs.py
• select_taxa.py
• sgt_constructor.py
• taxon_collapser.py
• vba_extract.py
• windowmasker_2.2.22_adapter.py
• working_dataset_constructor.py

Module

You can load the modules by:

module load biocontainers
module load phylofisher

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 phylofisher on our clusters:

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

module --force purge
ml biocontainers phylofisher