Goatools
is a python library for gene ontology analyses. Detailed information about its usage can be found here: https://github.com/tanghaibao/goatools
- 1.1.12
- 1.2.3
- 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
You can load the modules by:
module load biocontainers module load goatools/1.1.12
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()
Warning
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