bioconvert.rst

Bioconvert

Introduction ~~~~~~~~ Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

For more information, please check its website: https://biocontainers.pro/tools/bioconvert and its home page: https://bioconvert.readthedocs.io/en/master/.

Versions

• 0.4.3
• 0.5.2
• 0.6.1
• 0.6.2

Commands ~~~~~~~ - bioconvert

Module

You can load the modules by:

module load biocontainers
module load bioconvert

Example job ~~~~~ .. 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 run Bioconvert on our clusters:

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

module --force purge
ml biocontainers bioconvert

bioconvert fastq2fasta input.fastq output.fa