Difference between revisions of "TrinityRNASeq Guide"

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(Created page with "[http://trinityrnaseq.github.io/ Trinity] is a program for de-novo assembly of RNA-Seq transcripts from Illumina. ==Check Module Availability== To see which Trinity modules a...")
 
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[http://trinityrnaseq.github.io/ Trinity] is a program for de-novo assembly of RNA-Seq transcripts from Illumina.
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Please see [[Trinity Guide]]
 
 
==Check Module Availability==
 
To see which Trinity modules are available to the system, use the following command:
 
 
 
$ module avail trinityrnaseq
 
 
 
You should see all available modules in <code>trinityrnaseq/<version></code> format:
 
<code>
 
----------------------- /apps2/Modules/3.2.6/modulefiles -----------------------
 
trinityrnaseq/2014.04.13p1 trinityrnaseq/v2.0.2-2015
 
</code>
 
 
 
If the module list is empty please [[HPC_Help#Contact your administrators|contact your administrators]].
 
 
 
 
 
==Loading a Trinity Module==
 
You can load the default Trinity module as follows:
 
<code>
 
$ module load trinityrnaseq
 
</code>
 
 
 
To see which version is being used, do the following:
 
<code>
 
$ which Trinity
 
/apps2/trinityRNASeq/v2.0.2/trinityrnaseq-2.0.2/Trinity
 
</code>
 
 
 
 
 
If your program needs a specific version e.g., <code>trinityrnaseq/2014.04.13p1</code>, do the following:
 
<code>
 
$ module load trinityrnaseq/'''2014.04.13p1'''
 
</code>
 
 
 
After you load a module you can use it until you log out; you will need to load it again the next time you log in and run your program.
 
 
 
 
 
==Automatically Loading a Trinity Module==
 
If you frequently use a particular module (which is usual) you can do the following:
 
<code>
 
$ module initadd trinityrnaseq
 
</code>
 
Or, if you need a specific version,
 
<code>
 
$ module initadd trinityrnaseq/'''2014.04.13p1'''
 
</code>
 
 
 
Note that this auto-loading of the module will start from your ''next'' login session. Therefore if you need the module at the present session you will need to load the module using the <code>'''module load'''</code> command.
 
 
 
 
 
==Unloading the Trinity Module==
 
You can unload an already-loaded module as follows:
 
<code>
 
$ module unload trinityrnaseq
 
</code>
 
 
 
Or, to unload a specific version,
 
<code>
 
$ module unload trinityrnaseq/'''2014.04.13p1'''
 
</code>
 
 
 
To make sure that a module is unloaded, use the command <code>'''which trinityrnaseq'''</code> which should say <code>/usr/bin/which: no trinityrnaseq in ...</code>
 
 
 
 
 
==Running Trinity==
 
After loading the module you can run Trinity as follows:
 
 
 
<code>
 
$ Trinity <options>
 
</code>
 
 
 
[[Category:Software]]
 

Latest revision as of 16:21, 9 September 2015

Please see Trinity Guide