Command line tool for prepare database for NGS analysis.
Currently only support Ensembl database.
git clone https://github.com/bioShaun/OMdatabase.git
cd OMdatabase
pip install .
oms_database --help
Usage: oms_database [OPTIONS]
Command line tool for prepare database for NGS analysis
Options:
-s, --species TEXT Species latin name. [required]
-d, --database TEXT Public database name.
-v, --version TEXT Database version.
-a, --analysis TEXT Analysis for which the database is build for.
-r, --run [download|build] Choose to download, build or update
-l, --launch [local|slurm] Choose to launch job local or on slurm.
--help Show this message and exit.
Usage Examples:
# Download ensembl annotation for aspergillus nidulans
oms_database -s aspergillus_nidulans -r download
# Download and build database for arabidopsis thaliana
oms_database -s arabidopsis_thaliana -r build