PAML-Teaching: Difference between revisions
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=== Version === | === Version === | ||
4. | 4.9j, 4.10.5 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Running Program === | === Running Program === | ||
Version 4.9j of this application is at /apps/eb/PAML/4.9j-GCC-11.2.0 | |||
To use this version, please | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml PAML/4. | ml PAML/4.9j-GCC-11.2.0 | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
<div class="gscript2"> | <div class="gscript2"> | ||
| Line 40: | Line 40: | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=PAML.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=PAML.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=PAML.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml PAML/4. | ml PAML/4.9j-GCC-11.2.0<br> | ||
baseml <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. | ||
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=== Documentation === | === Documentation === | ||
Please see http://abacus.gene.ucl.ac.uk/software/paml.html | |||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
Latest revision as of 15:47, 13 May 2024
Category
Bioinformatics
Program On
Teaching
Version
4.9j, 4.10.5
Author / Distributor
Description
"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood." More details are at PAML
Running Program
Version 4.9j of this application is at /apps/eb/PAML/4.9j-GCC-11.2.0
To use this version, please load the module with
ml PAML/4.9j-GCC-11.2.0
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_PAML
#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=PAML.%j.out
#SBATCH --error=PAML.%j.err
cd $SLURM_SUBMIT_DIR
ml PAML/4.9j-GCC-11.2.0
baseml [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 http://abacus.gene.ucl.ac.uk/software/paml.html
Installation
Source code is obtained from PAML
System
64-bit Linux