Stacks-Teaching: Difference between revisions
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=== Version === | === Version === | ||
2.0 | |||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/eb/Stacks/ | The last version of this application is at /usr/local/apps/eb/Stacks/2.0-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 Stacks/ | ml Stacks/2.0-foss-2016b | ||
</pre> | </pre> | ||
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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=Stacks.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=Stacks.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=Stacks.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml Stacks/ | ml Stacks/2.0-foss-2016b<br> | ||
sstacks <u>[options]</u><br> | sstacks <u>[options]</u><br> | ||
</div> | </div> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml Stacks/ | ml Stacks/2.0-foss-2016b | ||
sstacks -h | |||
sstacks | sstacks 2.0 | ||
sstacks | sstacks -P dir -M popmap [-p n_threads] | ||
sstacks | sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] | ||
-P,--in_path: path to the directory containing Stacks files. | |||
-M,--popmap: path to a population map file from which to take sample names. | |||
M: path to a population map file from which to take sample names. | -s,--sample: filename prefix from which to load sample loci. | ||
s: filename prefix from which to load sample loci. | -c,--catalog: path to the catalog. | ||
c: path to the catalog. | -p,--threads: enable parallel execution with num_threads threads. | ||
-o,--out_path: output path to write results. | |||
-x: don't verify haplotype of matching locus. | |||
o: output path to write results. | |||
x: don't verify haplotype of matching locus. | |||
Gapped assembly options: | Gapped assembly options: | ||
-- | --disable_gapped: disable gapped alignments between stacks (default: enable gapped alignments). | ||
</pre> | </pre> | ||
Revision as of 14:10, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.0
Author / Distributor
Description
"Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography." More details are at Stacks
Running Program
The last version of this application is at /usr/local/apps/eb/Stacks/2.0-foss-2016b
To use this version, please load the module with
ml Stacks/2.0-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_Stacks
#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=Stacks.%j.out
#SBATCH --error=Stacks.%j.err
cd $SLURM_SUBMIT_DIR
ml Stacks/2.0-foss-2016b
sstacks [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 Stacks/2.0-foss-2016b sstacks -h sstacks 2.0 sstacks -P dir -M popmap [-p n_threads] sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] -P,--in_path: path to the directory containing Stacks files. -M,--popmap: path to a population map file from which to take sample names. -s,--sample: filename prefix from which to load sample loci. -c,--catalog: path to the catalog. -p,--threads: enable parallel execution with num_threads threads. -o,--out_path: output path to write results. -x: don't verify haplotype of matching locus. Gapped assembly options: --disable_gapped: disable gapped alignments between stacks (default: enable gapped alignments).
Installation
Source code is obtained from Stacks
System
64-bit Linux