Difference between revisions of "TrinityRNASeq Guide"
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To make sure that a module is unloaded, use the command <code>'''which
To make sure that a module is unloaded, use the command <code>'''which '''</code> which should say <code>/usr/bin/which: no in ...</code>
Revision as of 16:03, 9 September 2015
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
----------------------- /apps2/Modules/3.2.6/modulefiles ----------------------- trinityrnaseq/2014.04.13p1 trinityrnaseq/v2.0.2-2015
If the module list is empty please contact your administrators.
Loading a Trinity Module
Because Triniy needs
gcc to work you will need to load
gcc before you load the
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 /apps2/trinityRNASeq/v2.0.2/trinityrnaseq-2.0.2/Trinity
If your program needs a specific version e.g.,
trinityrnaseq/2014.04.13p1, 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
module load 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
which Trinity which should say
/usr/bin/which: no Trinity in ...
After loading the module you can run Trinity as follows:
$ Trinity <options>