PASA-Sapelo2 - Revision history

Shtsai at 01:18, 5 April 2026

2026-04-05T01:18:59Z

← Older revision		Revision as of 21:18, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	2.5.3		2.5.3

	=== Author / Distributor ===		== Author / Distributor ==
	https://github.com/PASApipeline/PASApipeline		https://github.com/PASApipeline/PASApipeline

	https://github.com/PASApipeline/PASApipeline/wiki		https://github.com/PASApipeline/PASApipeline/wiki

	=== Description ===		== Description ==
	"PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments."		"PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments."

	More details are at https://github.com/PASApipeline/PASApipeline/wiki		More details are at https://github.com/PASApipeline/PASApipeline/wiki

	=== Running Program ===		== Running Program ==

	* version 2.5.3 with MySQL support is installed as an Apptainer container in /apps/singularity-images/pasa-2.5.3-MySQL/. The image name is pasa-2.5.3-mysql-production.sif.		* version 2.5.3 with MySQL support is installed as an Apptainer container in /apps/singularity-images/pasa-2.5.3-MySQL/. The image name is pasa-2.5.3-mysql-production.sif.
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	</pre>		</pre>

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

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	Source code is obtained from https://github.com/PASApipeline/PASApipeline		Source code is obtained from https://github.com/PASApipeline/PASApipeline

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

Moses at 15:53, 16 June 2025

2025-06-16T15:53:48Z

← Older revision		Revision as of 11:53, 16 June 2025
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	* Sample batch job submission script: '''sub.sh'''		* Sample batch job submission script: '''sub.sh'''
	* Sample data folder provided by PASA : '''sample_data/'''		* Sample data folder provided by PASA : '''sample_data/'''
			Please note:

			* PASA requires an environment variable called PASAHOME. In this container it is defined as /opt/pasa/opt/pasa-2.5.3/ .
			* PASA's Perl scripts, for example, build_comprehensive_transcriptome.dbi, Load_Current_Gene_Annotations.dbi, and others, are installed in $PASAHOME'''/scripts/ .'''



	Below is the sample batch job submission script ('''sub.sh''') to run PASA (alignment assembly pipeline) in a batch job using 20 CPU cores on the batch partition:		Below is the sample batch job submission script ('''sub.sh''') to run PASA (alignment assembly pipeline) in a batch job using 20 CPU cores on the batch partition:

Moses at 14:01, 5 June 2025

2025-06-05T14:01:30Z

← Older revision		Revision as of 10:01, 5 June 2025
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	'''--CPU <u>20</u> \'''<br>		'''--CPU <u>20</u> \'''<br>
	'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''<br>		'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''<br>
	'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''		'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''<br>
	<br>
	<br>		<br>
	<nowiki>#</nowiki> Clean up on the compute node and shut down MySQL		<nowiki>#</nowiki> Clean up on the compute node and shut down MySQL

Moses at 14:00, 5 June 2025

2025-06-05T14:00:14Z

← Older revision		Revision as of 10:00, 5 June 2025
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	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
	<nowiki>#</nowiki>SBATCH --mail-user=<u>username</u>@uga.edu<br>		<nowiki>#</nowiki>SBATCH --mail-user=<u>username</u>@uga.edu<br>
			<br>
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
			<br>
			<br>
	<nowiki>#</nowiki> Initialize and start MySQL from inside of the container		<nowiki>#</nowiki> Initialize and start MySQL from inside of the container
			<br>
	./1_init.sh && ./2_create_user_and_db.sh		./1_init.sh && ./2_create_user_and_db.sh
			<br>
			<br>

	<nowiki>#</nowiki> unzip the sample input date genome_sample.fasta.gz		<nowiki>#</nowiki> unzip the sample input date genome_sample.fasta.gz
			<br>
	gunzip sample_data/genome_sample.fasta.gz		gunzip sample_data/genome_sample.fasta.gz
			<br>
			<br>
	<nowiki>#</nowiki> Run PASA pipeline with genome_sample.fasta		<nowiki>#</nowiki> Run PASA pipeline with genome_sample.fasta
			<br>
	apptainer exec instance://pasa-mysql /bin/bash -c "source activate /opt/pasa && \$PASAHOME/Launch_PASA_pipeline.pl \		apptainer exec instance://pasa-mysql /bin/bash -c "source activate /opt/pasa && \$PASAHOME/Launch_PASA_pipeline.pl \<br>
			'''--CPU <u>20</u> \'''<br>
	'''--CPU <u>20</u> \'''		'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''<br>

	'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''

	'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''		'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''
			<br>
			<br>

	<nowiki>#</nowiki> Clean up on the compute node and shut down MySQL		<nowiki>#</nowiki> Clean up on the compute node and shut down MySQL
			<br>
	./3_cleanup.sh		./3_cleanup.sh

Moses at 13:56, 5 June 2025

2025-06-05T13:56:49Z

← Older revision		Revision as of 09:56, 5 June 2025
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	apptainer exec instance://pasa-mysql /bin/bash -c "source activate /opt/pasa && \$PASAHOME/Launch_PASA_pipeline.pl \		apptainer exec instance://pasa-mysql /bin/bash -c "source activate /opt/pasa && \$PASAHOME/Launch_PASA_pipeline.pl \

	'''--CPU <u>20</u> \'''		'''--CPU <u>20</u> \'''

	'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''		'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''

	'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''		'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''

Moses at 13:56, 5 June 2025

2025-06-05T13:56:07Z

← Older revision		Revision as of 09:56, 5 June 2025
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	apptainer exec instance://pasa-mysql /bin/bash -c "source activate /opt/pasa && \$PASAHOME/Launch_PASA_pipeline.pl \		apptainer exec instance://pasa-mysql /bin/bash -c "source activate /opt/pasa && \$PASAHOME/Launch_PASA_pipeline.pl \

	'''--CPU <u>20</u> \'''		'''--CPU <u>20</u> \'''

	'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''		'''--config ./sample_data/mysql.confs/alignAssembly.config --create --run \'''

	'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''		'''--ALIGNER gmap --genome ./sample_data/genome_sample.fasta --transcripts ./sample_data/all_transcripts.fasta.clean"'''

Moses at 13:54, 5 June 2025

2025-06-05T13:54:54Z

← Older revision		Revision as of 09:54, 5 June 2025
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	./1_init.sh && ./2_create_user_and_db.sh		./1_init.sh && ./2_create_user_and_db.sh
	~~<nowiki>#</nowiki> unzip the sample input date genome_sample.fasta.gz~~

Moses: /* Running Program */

2025-06-05T13:53:40Z

Running Program

← Older revision		Revision as of 09:53, 5 June 2025
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	* version 2.5.3 with MySQL support is installed as an Apptainer container in /apps/singularity-images/pasa-2.5.3-MySQL/. The image name is pasa-2.5.3-mysql-production.sif.		* version 2.5.3 with MySQL support is installed as an Apptainer container in /apps/singularity-images/pasa-2.5.3-MySQL/. The image name is pasa-2.5.3-mysql-production.sif.

	To use this version of PASA ~~with its sample data~~ in a batch job, please follow these setup steps in your current job working directory '''before''' submitting a batch job:		To use this version of PASA in a batch job, please follow these setup steps in your current job working directory '''before''' submitting a batch job:

	<pre class="gscript">		<pre class="gscript">
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	Note:		Note:

	Running the above cp commands will copy the following setup files and ~~folder~~ to your current ~~job~~ working directory:		Running the above cp commands will copy the following setup files and folders to your current working directory:

	* Three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh'''		* Three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh'''
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	Below is the sample batch job submission script ('''sub.sh''') to run PASA in a batch job using 20 CPU cores on the batch partition:		Below is the sample batch job submission script ('''sub.sh''') to run PASA (alignment assembly pipeline) in a batch job using 20 CPU cores on the batch partition:

	<div class="gscript2">		<div class="gscript2">

Moses: /* Running Program */

2025-06-05T13:50:55Z

Running Program

← Older revision		Revision as of 09:50, 5 June 2025
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	=== Running Program ===		=== Running Program ===

	* version 2.5.3 with MySQL support is installed as an Apptainer container in /apps/singularity-images/pasa-2.5.3-MySQL/ ~~and the~~ image name is pasa-2.5.3-mysql-production.sif.		* version 2.5.3 with MySQL support is installed as an Apptainer container in /apps/singularity-images/pasa-2.5.3-MySQL/. The image name is pasa-2.5.3-mysql-production.sif.

	To use this version of PASA with its sample data in a batch job, please follow these setup steps in your current job working directory '''before''' submitting a batch job:		To use this version of PASA with its sample data in a batch job, please follow these setup steps in your current job working directory '''before''' submitting a batch job:
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	<pre class="gscript">		<pre class="gscript">
	mkdir ./workDir		mkdir ./workDir
	cd ./workDir		cd workDir
	cp -r /apps/singularity-images/pasa-2.5.3-MySQL/{1_init.sh,2_create_user_and_db.sh,3_cleanup.sh,pasa_conf,sub.sh,sample_data} .		cp -r /apps/singularity-images/pasa-2.5.3-MySQL/{1_init.sh,2_create_user_and_db.sh,3_cleanup.sh,pasa_conf,sub.sh,sample_data} .
	</pre>		</pre>

Moses: /* Author / Distributor */

2025-06-05T13:50:15Z

Author / Distributor

← Older revision		Revision as of 09:50, 5 June 2025
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	=== Author / Distributor ===		=== Author / Distributor ===
	https://github.com/PASApipeline/PASApipeline		https://github.com/PASApipeline/PASApipeline

	https://github.com/PASApipeline/PASApipeline/wiki		https://github.com/PASApipeline/PASApipeline/wiki

	=== Description ===		=== Description ===
	"PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments."		"PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments."