Cactus-Sapelo2 - Revision history

Shtsai at 00:20, 5 April 2026

2026-04-05T00:20:44Z

← Older revision		Revision as of 20:20, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics
	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2
	=== Version ===		== 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		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
	===Description===		==Description==
	From https://github.com/ComparativeGenomicsToolkit/cactus: "Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit."		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 ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	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.		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 ==

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

	=== Installation ===		== Installation ==

	Singularity images built from the docker container provided by the authors. For example:		Singularity images built from the docker container provided by the authors. For example:
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	singularity pull docker://quay.io/comparative-genomics-toolkit/cactus:v2.7.0-gpu		singularity pull docker://quay.io/comparative-genomics-toolkit/cactus:v2.7.0-gpu

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea: /* Program On */

2024-05-09T14:25:35Z

Program On

← Older revision		Revision as of 10:25, 9 May 2024
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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

Shtsai: /* Running Program */

2024-01-03T17:24:26Z

Running Program

← Older revision		Revision as of 13:24, 3 January 2024
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	To run the commands in the singularity containers, please ~~bind mount~~ /~~run/user~~. ~~For example,~~		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 -B /~~run~~/~~user~~ /apps/singularity-images/cactus_v2.7.0.sif cactus [options]		export CACTUS_TMPDIR=/lscratch/$USER/cactus-$SLURM_JOB_ID
	~~</pre>~~		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]

	or		cd /lscratch/$USER
			rm -r -f cactus-$SLURM_JOB_ID

	~~<pre class="gcommand">~~
	~~singularity exec -B /run/user /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome [options]~~
	</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 -B /~~run~~/~~user~~ /apps/singularity-images/cactus_v2.7.0.sif cactus ~~[options]~~		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 [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.		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 ===

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.6.7, 2.6.9, 2.7.0 ===Author..."

2023-12-23T02:09:47Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.6.7, 2.6.9, 2.7.0 ===Author..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== 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,

<pre class="gcommand">
singularity exec -B /run/user /apps/singularity-images/cactus_v2.7.0.sif cactus [options]
</pre>

or

<pre class="gcommand">
singularity exec -B /run/user /apps/singularity-images/cactus_v2.7.0.sif cactus-pangenome [options]
</pre>

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

<pre class="gscript">
#!/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]

</pre>
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