Cactus-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.6.7, 2.6.9, 2.7.0

Author / Distributor

Please see https://github.com/ComparativeGenomicsToolkit/cactus

Description

From https://github.com/ComparativeGenomicsToolkit/cactus: "Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit."

Running Program

Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo2 please see the Lmod page.

• Version 2.6.7 is installed as module called Cactus/2.6.7-GCCcore-11.3.0-Python-3.10.4

• Version 2.6.9 is installed as a singularity image at /apps/singularity-images/cactus_v2.6.9.sif

• Version 2.7.0 is installed as a singularity image at /apps/singularity-images/cactus_v2.7.0.sif

• Version 2.7.0 with GPU support is installed as a singularity image at /apps/singularity-images/cactus_v2.7.0-gpu.sif

To run the commands in the singularity containers, please bind mount /run/user. For example,

singularity exec -B /run/user /apps/singularity-images/cactus_v2.7.0.sif cactus [options]

or

singularity exec -B /run/user /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome [options]

Sample job submission script (sub.sh) to run cactus version 2.7.0:

#!/bin/bash
#SBATCH --job-name=testcactus         # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=5gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log

cd $SLURM_SUBMIT_DIR

singularity exec -B /run/user /apps/singularity-images/cactus_v2.7.0.sif cactus [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

Documentation

Please see https://github.com/ComparativeGenomicsToolkit/cactus

Installation

Singularity images built from the docker container provided by the authors. For example:

singularity pull docker://quay.io/comparative-genomics-toolkit/cactus:v2.7.0

singularity pull docker://quay.io/comparative-genomics-toolkit/cactus:v2.7.0-gpu

System

64-bit Linux