Purdue University

Commands

• atoiindex
• cmetindex
• cpuid
• dbsnp_iit
• ensembl_genes
• fa_coords
• get-genome
• gff3_genes
• gff3_introns
• gff3_splicesites
• gmap
• gmap.avx2
• gmap_build
• gmap_cat
• gmapindex
• gmapl
• gmapl.avx2
• gmapl.nosimd
• gmap.nosimd
• gmap_process
• gsnap
• gsnap.avx2
• gsnapl
• gsnapl.avx2
• gsnapl.nosimd
• gsnap.nosimd
• gtf_genes
• gtf_introns
• gtf_splicesites
• gtf_transcript_splicesites
• gvf_iit
• iit_dump
• iit_get
• iit_store
• indexdb_cat
• md_coords
• psl_genes
• psl_introns
• psl_splicesites
• sam_sort
• snpindex
• trindex
• vcf_iit

Module

You can load the modules by:

module load biocontainers
module load gmap

Example 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 run Gmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=gmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gmap

gmap_build -d Cmm -D Cmm genome.fasta
gmap -d Cmm -t 4 -D ./Cmm  cdna.fasta > gmap_out.txt

gmap_build -d GRCh38 -D GRCh38 Homo_sapiens.GRCh38.dna.primary_assembly.fa
gsnap -d GRCh38 -D ./GRCh38 --nthreads=4  SRR16956239_1.fastq SRR16956239_2.fastq > gsnap_out.txt