Biopython-Teaching: Difference between revisions

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=== Version ===
=== Version ===
1.68
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 /usr/local/apps/eb/Biopython/1.68-foss-2016b-Python-2.7.14
The last version of this application is at /apps/eb/Biopython/1.81-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/1.68-foss-2016b-Python-2.7.14
ml Biopython/1.79-foss-2022a
</pre>  
</pre>  


Line 43: Line 47:
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml Biopython/1.68-foss-2016b-Python-2.7.14<br>     
ml Biopython/1.79-foss-2022a<br>     
<u>[options]</u><br>   
python <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.   
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.   
Line 58: Line 62:
=== Documentation ===
=== Documentation ===
   
   
<pre  class="gcommand">
Please see https://biopython.org/
ml Biopython/1.68-foss-2016b-Python-2.7.14


</pre>
[[#top|Back to Top]]
[[#top|Back to Top]]



Latest revision as of 10:07, 9 May 2024

Category

Bioinformatics

Program On

Teaching

Version

1.75, 1.76, 1.78, 1.79, 1.81

Author / Distributor

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 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/

Back to Top

Installation

Source code is obtained from Biopython

System

64-bit Linux