ORP-Sapelo2 - Revision history

Shtsai at 01:15, 5 April 2026

2026-04-05T01:15:52Z

← Older revision		Revision as of 21:15, 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 ==
	2.2.6, 2.2.8, 2.3.3		2.2.6, 2.2.8, 2.3.3
	===Author / Distributor===		==Author / Distributor==
	Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html		Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html
	===Description===		==Description==
	From https://oyster-river-protocol.readthedocs.io/en/latest/index.html: "The Oyster River Protocol for (eukaryotic) transcriptome assembly is an actively developed, evidenced based method for optimizing transcriptome assembly. The manuscript corresponding to this protocol is here: https://peerj.com/articles/5428/ In brief, the protocol assembles the transcriptome using a multi-kmer multi-assembler approach, then merges those assemblies into 1 final assembly."		From https://oyster-river-protocol.readthedocs.io/en/latest/index.html: "The Oyster River Protocol for (eukaryotic) transcriptome assembly is an actively developed, evidenced based method for optimizing transcriptome assembly. The manuscript corresponding to this protocol is here: https://peerj.com/articles/5428/ In brief, the protocol assembles the transcriptome using a multi-kmer multi-assembler approach, then merges those assemblies into 1 final assembly."
	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.htm		Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.htm

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

Chelsea: /* Installation */

2025-04-02T16:19:22Z

Installation

← Older revision		Revision as of 12:19, 2 April 2025
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	=== Installation ===		=== Installation ===

	*Version 2.2.6, installed with <code>singularity pull docker://macmaneslab/orp:2.2.6</code>
	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Chelsea at 16:19, 2 April 2025

2025-04-02T16:19:01Z

← Older revision		Revision as of 12:19, 2 April 2025
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	*Version 2.2.6, installed in /apps/singularity-images/		*Version 2.3.3, installed in /apps/singularity-images/

	Sample job submission script (sub.sh) to run oyster.mk v. 2.3.3:		Sample job submission script (sub.sh) to run oyster.mk v. 2.3.3:

Chelsea at 16:18, 2 April 2025

2025-04-02T16:18:51Z

← Older revision		Revision as of 12:18, 2 April 2025
Line 5:		Line 5:
	Sapelo2		Sapelo2
	=== Version ===		=== Version ===
	2.2.6, 2.2.8		2.2.6, 2.2.8, 2.3.3
	===Author / Distributor===		===Author / Distributor===
	Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html		Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html
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	*Version 2.2.6, installed in /apps/singularity-images/		*Version 2.2.6, installed in /apps/singularity-images/

	Sample job submission script (sub.sh) to run oyster.mk v. 2.2.6:		Sample job submission script (sub.sh) to run oyster.mk v. 2.3.3:

	<pre class="gscript">		<pre class="gscript">
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	#SBATCH --mem=20gb		#SBATCH --mem=20gb

	singularity run /apps/singularity-images/orp_2.2.6.sif bash -c "source activate orp && /home/orp/Oyster_River_Protocol/oyster.mk \		singularity run /apps/singularity-images/orp_2.3.3_modified.sif bash --login -c "source activate orp && /home/orp/Oyster_River_Protocol/oyster.mk \
	STRAND=RF \		STRAND=RF \
	TPM_FILT=1 \		TPM_FILT=1 \

Chelsea: /* Version */

2024-05-13T20:45:16Z

Version

← Older revision		Revision as of 16:45, 13 May 2024
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	Sapelo2		Sapelo2
	=== Version ===		=== Version ===
	2.2.6		2.2.6, 2.2.8
	===Author / Distributor===		===Author / Distributor===
	Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html		Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html

Shtsai at 02:39, 16 September 2021

2021-09-16T02:39:28Z

← Older revision		Revision as of 22:39, 15 September 2021
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	[[Category:~~Sapelo2old~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		=== Category ===
	Bioinformatics		Bioinformatics

Shtsai: /* Running Program */

2021-01-07T02:49:43Z

Running Program

← Older revision		Revision as of 22:49, 6 January 2021
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	#!/bin/bash		#!/bin/bash
	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --~~jobn~~-name=jobname		#SBATCH --job-name=jobname
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
	#SBATCH --cpus-per-task=4		#SBATCH --cpus-per-task=4

Ben at 19:01, 6 January 2021

2021-01-06T19:01:46Z

← Older revision		Revision as of 15:01, 6 January 2021
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	STRAND=RF \		STRAND=RF \
	TPM_FILT=1 \		TPM_FILT=1 \
	MEM=20 \		MEM=15 \
	CPU=4 \		CPU=4 \
	READ1=test.1.fq.gz \		READ1=test.1.fq.gz \

Ben at 18:42, 6 January 2021

2021-01-06T18:42:40Z

← Older revision		Revision as of 14:42, 6 January 2021
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	#SBATCH --jobn-name=jobname		#SBATCH --jobn-name=jobname
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
			#SBATCH --cpus-per-task=4
	#SBATCH --time=4:00:00		#SBATCH --time=4:00:00
	#SBATCH --mem=20gb		#SBATCH --mem=20gb
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	STRAND=RF \		STRAND=RF \
	TPM_FILT=1 \		TPM_FILT=1 \
	MEM=5 \		MEM=20 \
	CPU=4 \		CPU=4 \
	READ1=test.1.fq.gz \		READ1=test.1.fq.gz \

Ben: Created page with "Category:Sapelo2oldCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.2.6 ===Author / Distribu..."

2021-01-06T18:41:47Z

Created page with "Category:Sapelo2old Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.2.6 ===Author / Distribu..."

New page

[[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===
Bioinformatics
=== Program On ===
Sapelo2
=== Version ===
2.2.6
===Author / Distributor===
Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html
===Description===
From https://oyster-river-protocol.readthedocs.io/en/latest/index.html: "The Oyster River Protocol for (eukaryotic) transcriptome assembly is an actively developed, evidenced based method for optimizing transcriptome assembly. The manuscript corresponding to this protocol is here: https://peerj.com/articles/5428/ In brief, the protocol assembles the transcriptome using a multi-kmer multi-assembler approach, then merges those assemblies into 1 final assembly."
=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

*Version 2.2.6, installed in /apps/singularity-images/

Sample job submission script (sub.sh) to run oyster.mk v. 2.2.6:

<pre class="gscript">
#!/bin/bash
#SBATCH --partition=batch
#SBATCH --jobn-name=jobname
#SBATCH --ntasks=1
#SBATCH --time=4:00:00
#SBATCH --mem=20gb

singularity run /apps/singularity-images/orp_2.2.6.sif bash -c "source activate orp && /home/orp/Oyster_River_Protocol/oyster.mk \
STRAND=RF \
TPM_FILT=1 \
MEM=5 \
CPU=4 \
READ1=test.1.fq.gz \
READ2=test.2.fq.gz \
RUNOUT=test "

</pre>
where test.1.fq.gz and test.2.fq.gz are sample data files and need to be replaced by your actual data files. 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.

Submit the job to the queue with
<pre class="gcommand">
sbatch sub.sh
</pre>

=== Documentation ===

Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.htm

=== Installation ===

*Version 2.2.6, installed with <code>singularity pull docker://macmaneslab/orp:2.2.6</code>
=== System ===
64-bit Linux