Biopython-Teaching - Revision history

Shtsai at 00:04, 5 April 2026

2026-04-05T00:04:01Z

← Older revision		Revision as of 20:04, 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 ==

	Teaching		Teaching

	=== 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 20:16, 7 July 2025

2025-07-07T20:16:16Z

← Older revision		Revision as of 16:16, 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<pre class="gscript">		To use this version with Python 3.12.3, please load the module with
	ml Biopython/1.81-foss-~~2022b~~		<pre class="gscript">
			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>

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

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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 */

2024-05-09T14:07:31Z

Version

← Older revision		Revision as of 10:07, 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/1.81-foss-2022b
	ml Biopython/1.79-foss-~~2021b~~
	</pre>		</pre>

Shtsai at 15:38, 5 September 2023

2023-09-05T15:38:28Z

← Older revision		Revision as of 11:38, 5 September 2023
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	=== Version ===		=== Version ===
	1.75		1.79

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

	The last version of this application is at /apps/eb/Biopython/1.75-foss-~~2019b-Python-3.7.4~~ and /apps/eb/Biopython/1.75-foss-~~2019b-Python-2.7.16~~		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 3.7.4, please load the module with		To use this version with Python 3.9.6, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.75-foss-~~2019b-Python-3.7.4~~		ml Biopython/1.79-foss-2021b
	</pre>		</pre>

	To use this version with Python 2.7.16, please load the module with		To use this version with Python 3.10.4, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.75-foss-~~2019b-Python-2.7.16~~		ml Biopython/1.79-foss-2022a
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml Biopython/1.75-foss-~~2019b-Python-2.7.16~~<br>		ml Biopython/1.79-foss-2022a<br>
	python <u>[options]</u><br>		python <u>[options]</u><br>
	</div>		</div>

Shtsai at 17:06, 27 August 2020

2020-08-27T17:06:14Z

@@ Line 9: / Line 9: @@
 === Version ===
-.68
+.75
 === Author / Distributor ===
@@ Line 21: / Line 21: @@
 === Running Program ===
-The last version of this application is at /usr/local/apps/eb/Biopython/1.68-foss-2016b-Python-2.7.14
+The last version of this application is at /apps/eb/Biopython/1.75-foss-2019b-Python-3.7.4 and /apps/eb/Biopython/1.75-foss-2019b-Python-2.7.16
-To use this version, please load the module with
+To use this version with Python 3.7.4, please load the module with
 <pre class="gscript">
-ml Biopython/1.68-foss-2016b-Python-2.7.14
+ml Biopython/1.75-foss-2019b-Python-3.7.4
 </pre>
@@ Line 43: / Line 48: @@
 cd $SLURM_SUBMIT_DIR<br>
-ml Biopython/1.68-foss-2016b-Python-2.7.14<br>
+ml Biopython/1.75-foss-2019b-Python-2.7.16<br>
 python <u>[options]</u><br>
 </div>
@@ Line 58: / Line 63: @@
 === Documentation ===
-<pre  class="gcommand">
+Please see https://biopython.org/
 [[#top|Back to Top]]

Yhuang at 16:19, 15 August 2018

2018-08-15T16:19:06Z

@@ Line 27: / Line 27: @@
 ml Biopython/1.68-foss-2016b-Python-2.7.14
 </pre>
 Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.
 === Documentation ===
@@ Line 34: / Line 60: @@
 <pre  class="gcommand">
 ml Biopython/1.68-foss-2016b-Python-2.7.14
+python -h
 </pre>

Yhuang at 18:43, 10 August 2018

2018-08-10T18:43:31Z

@@ Line 27: / Line 27: @@
 ml Biopython/1.68-foss-2016b-Python-2.7.14
 </pre>
 Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.
 === Documentation ===

Yhuang at 18:02, 10 August 2018

2018-08-10T18:02:17Z

← Older revision		Revision as of 14:02, 10 August 2018
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	<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
	<nowiki>#</nowiki>SBATCH --output=Biopython.%j.out<br>		<nowiki>#</nowiki>SBATCH --output=Biopython.%j.out<br>
			<nowiki>#</nowiki>SBATCH --error=Biopython.%j.err<br>

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
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	<pre class="gcommand">		<pre class="gcommand">
	ml Biopython/1.68-foss-2016b-Python-2.7.14		ml Biopython/1.68-foss-2016b-Python-2.7.14


	</pre>		</pre>

Yhuang at 17:41, 10 August 2018

2018-08-10T17:41:25Z

← Older revision		Revision as of 13:41, 10 August 2018
Line 23:		Line 23:
	The last version of this application is at /usr/local/apps/eb/Biopython/1.68-foss-2016b-Python-2.7.14		The last version of this application is at /usr/local/apps/eb/Biopython/1.68-foss-2016b-Python-2.7.14

	To use this version, please ~~loads~~ the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.68-foss-2016b-Python-2.7.14		ml Biopython/1.68-foss-2016b-Python-2.7.14
	</pre>		</pre>

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

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

Yhuang at 15:32, 10 August 2018

2018-08-10T15:32:41Z

← Older revision		Revision as of 11:32, 10 August 2018
Line 25:		Line 25:
	To use this version, please loads the module with		To use this version, please loads the module with
	<pre class="gscript">		<pre class="gscript">
	ml Biopython/1.68-foss-2016b-Python-2.7.14		ml Biopython/1.68-foss-2016b-Python-2.7.14


	</pre>		</pre>

Line 44:		Line 42:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
			ml Biopython/1.68-foss-2016b-Python-2.7.14<br>
	ml <!-- ~~TEST_COMMAND BEGIN~~ --><~~!-- TEST_COMMAND END --~~> <u>[options]</u><br>		<u>[options]</u><br>
	</div>		</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 ~~or be reviewed~~ .		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_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.		Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.
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	<pre class="gcommand">		<pre class="gcommand">
	Biopython/1.68-foss-2016b-Python-2.7.14		ml Biopython/1.68-foss-2016b-Python-2.7.14


	</pre>		</pre>