PAML-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=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> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml PAML/4.9h-foss-2016b | ml PAML/4.9h-foss-2016b | ||
which baseml | |||
/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml | /usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml | ||
Revision as of 13:04, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
4.9h
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
The last version of this application is at /usr/local/apps/eb/PAML/4.9h-foss-2016b
To use this version, please load the module with
ml PAML/4.9h-foss-2016b
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/4.9h-foss-2016b
which 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
ml PAML/4.9h-foss-2016b which baseml /usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml
Installation
Source code is obtained from PAML
System
64-bit Linux