Stacks-Teaching: Difference between revisions

From Research Computing Center Wiki
Jump to navigation Jump to search
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.48 === Au...")
 
No edit summary
Line 9: Line 9:


=== Version ===
=== Version ===
1.48
2.0
   
   
=== Author / Distributor ===
=== Author / Distributor ===
Line 21: Line 21:
=== Running Program ===
=== Running Program ===


The last version of this application is at /usr/local/apps/eb/Stacks/1.48-foss-2016b
The last version of this application is at /usr/local/apps/eb/Stacks/2.0-foss-2016b


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 Stacks/1.48-foss-2016b
ml Stacks/2.0-foss-2016b  
 
sstacks
</pre>  
</pre>  


Line 44: Line 42:
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
 
ml Stacks/2.0-foss-2016b<br>  
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u><br>   
sstacks <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 or be reviewed .   
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">
Stacks/1.48-foss-2016b
ml Stacks/2.0-foss-2016b  
sstacks -h
sstacks sstacks -h
sstacks 1.48
sstacks 2.0
sstacks [--aligned] -P dir [-b batch_id] -M popmap [-p n_threads]
sstacks -P dir -M popmap [-p n_threads]
sstacks [--aligned] -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads]
sstacks -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,--in_path: path to the directory containing Stacks files.
  P: 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.
   g,--aligned: base matching on alignment position, not sequence identity.
   -o,--out_path: output path to write results.
  p: enable parallel execution with num_threads threads.
   -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:
   --gapped: preform gapped alignments between stacks.
   --disable_gapped: disable gapped alignments between stacks (default: enable gapped alignments).


</pre>
</pre>

Revision as of 10:37, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

2.0

Author / Distributor

Stacks

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 loads the module with 

ml Stacks/2.0-foss-2016b

Here is an example of a shell script, sub.sh, to run on at 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/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 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).

Back to Top

Installation

Source code is obtained from Stacks

System

64-bit Linux

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=Stacks-Teaching&oldid=13062"