Commands

• python
• python3
• compare_gos.py
• fetch_associations.py
• find_enrichment.py
• go_plot.py
• map_to_slim.py
• ncbi_gene_results_to_python.py
• plot_go_term.py
• prt_terms.py
• runxlrd.py
• vba_extract.py
• wr_hier.py
• wr_sections.py

Module

You can load the modules by:

module load biocontainers  
module load goatools/1.1.12

Interactive job

To run goatools interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers goatools/1.1.12
(base) UserID@bell-a008:~ $ python
Python 3.8.10 (default, Nov 26 2021, 20:14:08)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.  
>>> from goatools.base import download_go_basic_obo
>>> obo_fname = download_go_basic_obo()

Batch 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 submit a sbatch job on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=goatools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers goatools/1.1.12

python script.py

find_enrichment.py --pval=0.05 --indent data/study data/population data/association

go_plot.py --go_file=tests/data/go_plot/go_heartjogging6.txt -r -o heartjogging6_r1.png