Biopython-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1. | 1.75, 1.76, 1.78, 1.79, 1.81 | ||
=== Author / Distributor === | === Author / Distributor === | ||
| Line 21: | Line 21: | ||
=== Running Program === | === Running Program === | ||
The last version of this application is at / | 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, please load the module with | To use this version with Python 3.10.8, please load the module with<pre class="gscript"> | ||
ml Biopython/1.81-foss-2022b | |||
</pre> | |||
To use this version with Python 3.10.4, please load the module with | |||
<pre class="gscript"> | <pre class="gscript"> | ||
ml Biopython/1. | ml Biopython/1.79-foss-2022a | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on the batch queue: | |||
<div class="gscript2"> | |||
<nowiki>#</nowiki>!/bin/bash<br> | |||
<nowiki>#</nowiki>SBATCH --job-name=j_Biopython<br> | |||
<nowiki>#</nowiki>SBATCH --partition=batch<br> | |||
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | |||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | |||
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> | |||
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br> | |||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | |||
<nowiki>#</nowiki>SBATCH --output=Biopython.%j.out<br> | |||
<nowiki>#</nowiki>SBATCH --error=Biopython.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | |||
ml Biopython/1.79-foss-2022a<br> | |||
python <u>[options]</u><br> | |||
</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_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. | ||
Here is an example of job submission command: | |||
<pre class="gcommand"> | |||
sbatch ./sub.sh | |||
</pre> | |||
=== Documentation === | === Documentation === | ||
Please see https://biopython.org/ | |||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
Latest revision as of 09:07, 9 May 2024
Category
Bioinformatics
Program On
Teaching
Version
1.75, 1.76, 1.78, 1.79, 1.81
Author / Distributor
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 Biopython
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
To use this version with Python 3.10.8, please load the module with
ml Biopython/1.81-foss-2022b
To use this version with Python 3.10.4, please load the module with
ml Biopython/1.79-foss-2022a
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_Biopython
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Biopython.%j.out
#SBATCH --error=Biopython.%j.err
cd $SLURM_SUBMIT_DIR
ml Biopython/1.79-foss-2022a
python [options]
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, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
Please see https://biopython.org/
Installation
Source code is obtained from Biopython
System
64-bit Linux