Biopython-Teaching: Difference between revisions
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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> | ||
Revision as of 14:02, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
1.68
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 /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
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/1.68-foss-2016b-Python-2.7.14
[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
ml Biopython/1.68-foss-2016b-Python-2.7.14
Installation
Source code is obtained from Biopython
System
64-bit Linux