The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software.

• https://github.com/genometools/genometools

• Module Name: genometools (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load genometools

[user@cn3144 ~]$ gt -help
Usage: bin/gt [option ...] [tool | script] [argument ...]
The GenomeTools genome analysis system.

-i       enter interactive mode after executing 'tool' or 'script'
-q       suppress warnings
-test    perform unit tests and exit
-seed    set seed for random number generator manually.
         0 generates a seed from current time and process id
-help    display help and exit
-version display version information and exit

Tools:

bed_to_gff3
cds
chain2dim
chseqids
clean
...
...

[user@cn3144 ~]$ gt bed_to_gff3 -help
Usage: bin/gt bed_to_gff3 [BED_file]
Parse BED file and convert it to GFF3.

-featuretype Set type of parsed BED features
             default: BED_feature
-thicktype   Set type of parsed thick BED features
             default: BED_thick_feature
-blocktype   Set type of parsed BED blocks
             default: BED_block
-o           redirect output to specified file
             default: undefined
-gzip        write gzip compressed output file
             default: no
-bzip2       write bzip2 compressed output file
             default: no
-force       force writing to output file
             default: no
-help        display help and exit
-version     display version information and exit

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. gt.sh). For example:

#!/bin/bash
set -e
module load genometools
cd /data/$USER
gt bed_to_gff3 -force yes -o out.gff3 input.bed

Submit this job using the Slurm sbatch command.

sbatch --mem=5g gt.sh

Create a swarmfile (e.g. gt.swarm). For example:

cd dir1; gt bed_to_gff3 -force yes -o out.gff3 input.bed
cd dir2; gt bed_to_gff3 -force yes -o out.gff3 input.bed
...
cd dir10; gt bed_to_gff3 -force yes -o out.gff3 input.bed

Submit this job using the swarm command.

swarm -f gt.swarm -g 5 --module gt