SAMtools-Teaching: Difference between revisions
No edit summary |
No edit summary |
||
| Line 9: | Line 9: | ||
=== Version === | === Version === | ||
1. | 0.1.19 | ||
=== Author / Distributor === | === Author / Distributor === | ||
| Line 16: | Line 16: | ||
=== Description === | === Description === | ||
"SAM Tools provide various utilities for manipulating alignments in the SAM format, | "SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." | ||
More details are at [http://www.htslib.org/ SAMtools] | More details are at [http://www.htslib.org/ SAMtools] | ||
=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/eb/SAMtools/1. | The last version of this application is at /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b | ||
To use this version, please load the module with | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml SAMtools/1. | ml SAMtools/0.1.19-foss-2016b | ||
</pre> | </pre> | ||
| Line 43: | Line 43: | ||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml SAMtools/1. | ml SAMtools/0.1.19-foss-2016b<br> | ||
samtools <u>[options]</u><br> | samtools <u>[options]</u><br> | ||
</div> | </div> | ||
| Line 59: | Line 59: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml SAMtools/1. | ml SAMtools/0.1.19-foss-2016b | ||
samtools --help | samtools --help | ||
[main] unrecognized command '--help' | |||
</pre> | </pre> | ||
Revision as of 14:08, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
0.1.19
Author / Distributor
Description
"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." More details are at SAMtools
Running Program
The last version of this application is at /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b
To use this version, please load the module with
ml SAMtools/0.1.19-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_SAMtools
#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=SAMtools.%j.out
#SBATCH --error=SAMtools.%j.err
cd $SLURM_SUBMIT_DIR
ml SAMtools/0.1.19-foss-2016b
samtools [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 SAMtools/0.1.19-foss-2016b samtools --help [main] unrecognized command '--help'
Installation
Source code is obtained from SAMtools
System
64-bit Linux