Stacks-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1.48 | |||
=== 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/1.48-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/1.48-foss-2016b | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml Stacks/ | ml Stacks/1.48-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/1.48-foss-2016b | ||
sstacks sstacks -h | sstacks sstacks -h | ||
sstacks | sstacks 1.48 | ||
sstacks -P dir -M popmap [-p n_threads] | sstacks [--aligned] -P dir [-b batch_id] -M popmap [-p n_threads] | ||
sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] | sstacks [--aligned] -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] | ||
b: database/batch ID of the catalog to consider (default: guess). | |||
P: path to the directory containing Stacks files. | |||
M: path to a population map file from which to take sample names. | |||
s: filename prefix from which to load sample loci. | |||
c: path to the catalog. | |||
g,--aligned: base matching on alignment position, not sequence identity. | |||
p: enable parallel execution with num_threads threads. | |||
o: output path to write results. | |||
x: don't verify haplotype of matching locus. | |||
Gapped assembly options: | Gapped assembly options: | ||
-- | --gapped: preform gapped alignments between stacks. | ||
</pre> | </pre> |
Revision as of 13:49, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
1.48
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/1.48-foss-2016b
To use this version, please load the module with
ml Stacks/1.48-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
cd $SLURM_SUBMIT_DIR
ml Stacks/1.48-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/1.48-foss-2016b sstacks sstacks -h sstacks 1.48 sstacks [--aligned] -P dir [-b batch_id] -M popmap [-p n_threads] sstacks [--aligned] -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] b: database/batch ID of the catalog to consider (default: guess). P: path to the directory containing Stacks files. M: path to a population map file from which to take sample names. s: filename prefix from which to load sample loci. c: path to the catalog. g,--aligned: base matching on alignment position, not sequence identity. p: enable parallel execution with num_threads threads. o: output path to write results. x: don't verify haplotype of matching locus. Gapped assembly options: --gapped: preform gapped alignments between stacks.
Installation
Source code is obtained from Stacks
System
64-bit Linux