Cactus-Sapelo2: Difference between revisions
(Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.6.7, 2.6.9, 2.7.0 ===Author...") |
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Sapelo2 | Sapelo2 | ||
=== Version === | === Version === | ||
2.6.7, 2.6.9, 2.7.0 | 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0 | ||
===Author / Distributor=== | ===Author / Distributor=== | ||
Please see https://github.com/ComparativeGenomicsToolkit/cactus | Please see https://github.com/ComparativeGenomicsToolkit/cactus | ||
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*Version 2.6.7 is installed as module called Cactus/2.6.7-GCCcore-11.3.0-Python-3.10.4 | *Version 2.6.7 is installed as module called Cactus/2.6.7-GCCcore-11.3.0-Python-3.10.4 | ||
*Version 1.2.3 is installed as a singularity image at /apps/singularity-images/cactus_v1.2.3.sif | |||
*Version 2.0.3 is installed as a singularity image at /apps/singularity-images/cactus_v2.0.3.sif | |||
*Version 2.4.3 is installed as a singularity image at /apps/singularity-images/cactus_v2.4.3.sif | |||
*Version 2.4.4 is installed as a singularity image at /apps/singularity-images/cactus_v2.4.4.sif | |||
*Version 2.5.0 is installed as a singularity image at /apps/singularity-images/cactus_v2.5.0.sif | |||
*Version 2.6.0 is installed as a singularity image at /apps/singularity-images/cactus_v2.6.0.sif | |||
*Version 2.6.9 is installed as a singularity image at /apps/singularity-images/cactus_v2.6.9.sif | *Version 2.6.9 is installed as a singularity image at /apps/singularity-images/cactus_v2.6.9.sif | ||
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To run the commands in the singularity containers, please | To run the commands in the singularity containers, please use an overlay for the /tmp partition. This can be done with the following steps: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
singularity exec - | export CACTUS_TMPDIR=/lscratch/$USER/cactus-$SLURM_JOB_ID | ||
mkdir -p -m 700 $CACTUS_TMPDIR/upper $CACTUS_TMPDIR/work | |||
truncate -s 300M jobStore.img | |||
apptainer exec /apps/singularity-images/cactus_v2.7.0.sif mkfs.ext3 -d $CACTUS_TMPDIR jobStore.img | |||
mkdir -m 700 -p $CACTUS_TMPDIR/tmp | |||
mkdir cactus_wd | |||
apptainer exec --cleanenv --overlay jobStore.img --bind $CACTUS_TMPDIR/tmp:/tmp \ | |||
--env PYTHONNOUSERSITE=1 /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome \ | |||
--workDir=cactus_wd [options] | |||
cd /lscratch/$USER | |||
rm -r -f cactus-$SLURM_JOB_ID | |||
</pre> | </pre> | ||
where the cactus-pangenome command in the example can be replaced by the cactus command. | |||
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cd $SLURM_SUBMIT_DIR | cd $SLURM_SUBMIT_DIR | ||
singularity exec - | export CACTUS_TMPDIR=/lscratch/$USER/cactus-$SLURM_JOB_ID | ||
mkdir -p -m 700 $CACTUS_TMPDIR/upper $CACTUS_TMPDIR/work | |||
truncate -s 300M jobStore.img | |||
apptainer exec /apps/singularity-images/cactus_v2.7.0.sif mkfs.ext3 -d $CACTUS_TMPDIR jobStore.img | |||
mkdir -m 700 -p $CACTUS_TMPDIR/tmp | |||
mkdir cactus_wd | |||
apptainer exec --cleanenv --overlay jobStore.img --bind $CACTUS_TMPDIR/tmp:/tmp \ | |||
--env PYTHONNOUSERSITE=1 /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome \ | |||
--workDir=cactus_wd ./js ./evolverPrimates.txt --outDir primates-pg --outName primates-pg \ | |||
--reference simChimp --vcf --giraffe --gfa --gbz | |||
cd /lscratch/$USER | |||
rm -r -f cactus-$SLURM_JOB_ID | |||
</pre> | </pre> | ||
where | where the sample options used here 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 === | === Documentation === |
Latest revision as of 10:25, 9 May 2024
Category
Bioinformatics
Program On
Sapelo2
Version
1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 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 1.2.3 is installed as a singularity image at /apps/singularity-images/cactus_v1.2.3.sif
- Version 2.0.3 is installed as a singularity image at /apps/singularity-images/cactus_v2.0.3.sif
- Version 2.4.3 is installed as a singularity image at /apps/singularity-images/cactus_v2.4.3.sif
- Version 2.4.4 is installed as a singularity image at /apps/singularity-images/cactus_v2.4.4.sif
- Version 2.5.0 is installed as a singularity image at /apps/singularity-images/cactus_v2.5.0.sif
- Version 2.6.0 is installed as a singularity image at /apps/singularity-images/cactus_v2.6.0.sif
- 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 use an overlay for the /tmp partition. This can be done with the following steps:
export CACTUS_TMPDIR=/lscratch/$USER/cactus-$SLURM_JOB_ID mkdir -p -m 700 $CACTUS_TMPDIR/upper $CACTUS_TMPDIR/work truncate -s 300M jobStore.img apptainer exec /apps/singularity-images/cactus_v2.7.0.sif mkfs.ext3 -d $CACTUS_TMPDIR jobStore.img mkdir -m 700 -p $CACTUS_TMPDIR/tmp mkdir cactus_wd apptainer exec --cleanenv --overlay jobStore.img --bind $CACTUS_TMPDIR/tmp:/tmp \ --env PYTHONNOUSERSITE=1 /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome \ --workDir=cactus_wd [options] cd /lscratch/$USER rm -r -f cactus-$SLURM_JOB_ID
where the cactus-pangenome command in the example can be replaced by the cactus command.
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 $SLURM_SUBMIT_DIR export CACTUS_TMPDIR=/lscratch/$USER/cactus-$SLURM_JOB_ID mkdir -p -m 700 $CACTUS_TMPDIR/upper $CACTUS_TMPDIR/work truncate -s 300M jobStore.img apptainer exec /apps/singularity-images/cactus_v2.7.0.sif mkfs.ext3 -d $CACTUS_TMPDIR jobStore.img mkdir -m 700 -p $CACTUS_TMPDIR/tmp mkdir cactus_wd apptainer exec --cleanenv --overlay jobStore.img --bind $CACTUS_TMPDIR/tmp:/tmp \ --env PYTHONNOUSERSITE=1 /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome \ --workDir=cactus_wd ./js ./evolverPrimates.txt --outDir primates-pg --outName primates-pg \ --reference simChimp --vcf --giraffe --gfa --gbz cd /lscratch/$USER rm -r -f cactus-$SLURM_JOB_ID
where the sample options used here 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