Keeko: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.9.6-1-centos_linux64, 2...."

2021-09-15T18:18:18Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.9.6-1-centos_linux64, 2...."

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[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2
=== Version ===
2.9.6-1-centos_linux64,
2.10.8-centos_linux64,
2.11.1-centos_linux64,

=== Author / Distributor ===

[https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc SRA-ToolKit]

=== Description ===
"The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives."
More details are at [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc SRA-ToolKit]

=== Running Program ===

The last version of this application is at /apps/eb/SRA-Toolkit/2.11.1-centos_linux64

To use this version, please load the module with
<pre class="gscript">
ml SRA-Toolkit/2.11.1-centos_linux64
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
ml ---------------- 
---- [options] 
</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.

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.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">

-----------------------------------
</pre>
[[#top|Back to Top]]

=== Installation ===

=== System ===
64-bit Linux

SRA-Toolkit - Revision history

Keeko: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.9.6-1-centos_linux64, 2...."