Difference between revisions of "RAxML-Teaching"
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 8.2.11 ===...") |
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To use this version, please loads the module with | To use this version, please loads the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
| − | ml RAxML/8.2.11-foss-2016b-mpi-sse3 | + | ml RAxML/8.2.11-foss-2016b-mpi-sse3 |
| − | |||
| − | |||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
| − | + | ml RAxML/8.2.11-foss-2016b-mpi-sse3<br> | |
| − | ml | + | raxmlHPC-PTHREADS-AVX <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. |
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. | ||
| Line 60: | Line 58: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
| − | RAxML/8.2.11-foss-2016b-mpi-sse3 | + | ml RAxML/8.2.11-foss-2016b-mpi-sse3 |
| − | raxmlHPC-PTHREADS-AVX -help | + | raxmlHPC-PTHREADS-AVX raxmlHPC-PTHREADS-AVX -help |
</pre> | </pre> | ||
Revision as of 11:35, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
8.2.11
Author / Distributor
Description
"RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." More details are at RAxML
Running Program
The last version of this application is at /usr/local/apps/eb/RAxML/8.2.11-foss-2016b-mpi-sse3
To use this version, please loads the module with
ml RAxML/8.2.11-foss-2016b-mpi-sse3
Here is an example of a shell script, sub.sh, to run on at the batch queue:
#!/bin/bash
#SBATCH --job-name=j_RAxML
#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=RAxML.%j.out
cd $SLURM_SUBMIT_DIR
ml RAxML/8.2.11-foss-2016b-mpi-sse3
raxmlHPC-PTHREADS-AVX [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 RAxML/8.2.11-foss-2016b-mpi-sse3 raxmlHPC-PTHREADS-AVX raxmlHPC-PTHREADS-AVX -help
Installation
Source code is obtained from RAxML
System
64-bit Linux