BioPython-Sapelo2 - Revision history

Shtsai at 00:03, 5 April 2026

2026-04-05T00:03:14Z

← Older revision		Revision as of 20:03, 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 ==
	1.79, 1.83, 1.84		1.79, 1.83, 1.84

	=== Author / Distributor ===		== Author / Distributor ==

	[http://www.biopython.org Biopython]		[http://www.biopython.org Biopython]

	=== Description ===		== Description ==
	"Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."		"Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."
	More details are at [http://www.biopython.org Biopython]		More details are at [http://www.biopython.org Biopython]

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

	The last version of this application is at /apps/eb/Biopython/1.84-foss-2024a		The last version of this application is at /apps/eb/Biopython/1.84-foss-2024a
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	</pre>		</pre>

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

	Please see https://biopython.org/		Please see https://biopython.org/
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	Source code is obtained from [http://www.biopython.org Biopython]		Source code is obtained from [http://www.biopython.org Biopython]

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

Chelsea at 20:14, 7 July 2025

2025-07-07T20:14:31Z

← Older revision		Revision as of 16:14, 7 July 2025
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	=== Version ===		=== Version ===
	1.~~75, 1.76, 1.78~~, 1.79, 1.81		1.79, 1.83, 1.84

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /apps/eb/Biopython/1.81-foss-~~2022b and /apps/eb/Biopython/1.81-foss-2022b~~		The last version of this application is at /apps/eb/Biopython/1.84-foss-2024a

	To use this version with Python 3.10.8, please load the module with		To use this version with Python 3.12.3, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.81-foss-~~2022b~~		ml Biopython/1.84-foss-2024a
	</pre>		</pre>

	To use this version with Python 3.10.4, please load the module with		To use this version with Python 3.11.5, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.79-foss-~~2022a~~		ml Biopython/1.84-foss-2023b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Biopython/1.79-foss-~~2022a~~<br>		ml Biopython/1.84-foss-2024a<br>
	python <u>[options]</u><br>		python <u>[options]</u><br>
	</div>		</div>

Chelsea: /* Version */

2024-05-09T14:04:25Z

Version

← Older revision		Revision as of 10:04, 9 May 2024
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	=== Version ===		=== Version ===
	1.79		1.75, 1.76, 1.78, 1.79, 1.81

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /apps/eb/Biopython/1.79-foss-~~2021b~~ and /apps/eb/Biopython/1.79-foss-~~2022a~~		The last version of this application is at /apps/eb/Biopython/1.81-foss-2022b and /apps/eb/Biopython/1.81-foss-2022b

	To use this version with Python 3.9.6, please load the module with		To use this version with Python 3.10.8, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.79-foss-~~2021b~~		ml Biopython/1.81-foss-2022b
	</pre>		</pre>

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.79 === Author / Distrib..."

2023-09-05T15:40:43Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.79 === Author / Distrib..."

New page

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

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.79

=== Author / Distributor ===

[http://www.biopython.org Biopython]

=== Description ===
"Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."
More details are at [http://www.biopython.org Biopython]

=== Running Program ===

The last version of this application is at /apps/eb/Biopython/1.79-foss-2021b and /apps/eb/Biopython/1.79-foss-2022a

To use this version with Python 3.9.6, please load the module with
<pre class="gscript">
ml Biopython/1.79-foss-2021b
</pre>

To use this version with Python 3.10.4, please load the module with
<pre class="gscript">
ml Biopython/1.79-foss-2022a
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Biopython 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Biopython.%j.out 
<nowiki>#</nowiki>SBATCH --error=Biopython.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Biopython/1.79-foss-2022a 
python [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_Sapelo2]] for more details of running jobs on Sapelo2.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

Please see https://biopython.org/

[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://www.biopython.org Biopython]

=== System ===
64-bit Linux