Biopython-Teaching: Difference between revisions

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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 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/1.68-foss-2016b-Python-2.7.14<br>   
<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 ===

Revision as of 13:43, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

1.68

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 /usr/local/apps/eb/Biopython/1.68-foss-2016b-Python-2.7.14

To use this version, please load the module with 

ml Biopython/1.68-foss-2016b-Python-2.7.14

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.

Documentation

ml Biopython/1.68-foss-2016b-Python-2.7.14

Back to Top

Installation

Source code is obtained from Biopython

System

64-bit Linux

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