Gmap

Introduction

Gmap is a genomic mapping and alignment program for mRNA and EST sequences.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/gmap
Home page: http://research-pub.gene.com/gmap/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2021.05.27, 2021.08.25

BELL

2021.05.27, 2021.08.25

GAUTSCHI

2021.05.27, 2021.08.25

NEGISHI

2021.05.27, 2021.08.25

SCHOLAR

2021.05.27, 2021.08.25

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

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 gmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers gmap

# Your gmap workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers gmap

# Your gmap workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers gmap

# Your gmap workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers gmap

# Your gmap workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers gmap

# Your gmap workflow...