Difference between revisions of "TrinityRNASeq Guide"

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Please see [[Trinity Guide]]
[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 are available to the system, use the following command:
$ module avail trinityrnaseq
You should see all available modules in <code>trinityrnaseq/<version></code> format:
----------------------- /apps2/Modules/3.2.6/modulefiles -----------------------
trinityrnaseq/2014.04.13p1 trinityrnaseq/v2.0.2-2015
If the module list is empty please [[HPC_Help#Contact your administrators|contact your administrators]].
==Loading a Trinity Module==
Because Triniy needs <code>gcc</code> to work you will need to load <code>gcc</code> before you load the <code>Trinity</code> module.
You can load the default Trinity module as follows:
$ module load gcc/4.7.1 trinityrnaseq
To see which version is being used, do the following:
$ which Trinity
If your program needs a specific version e.g., <code>trinityrnaseq/2014.04.13p1</code>, do the following:
$ module load gcc/4.7.1 trinityrnaseq/'''2014.04.13p1'''
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:
$ module initadd gcc/4.7.1 trinityrnaseq
Or, if you need a specific version,
$ module initadd gcc/4.7.1 trinityrnaseq/'''2014.04.13p1'''
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:
$ module unload trinityrnaseq
Or, to unload a specific version,
$ module unload trinityrnaseq/'''2014.04.13p1'''
To make sure that a module is unloaded, use the command <code>'''which Trinity'''</code> which should say <code>/usr/bin/which: no Trinity in ...</code>
==Running Trinity==
After loading the module you can run Trinity as follows:
$ Trinity <options>

Latest revision as of 16:21, 9 September 2015

Please see Trinity Guide