Trinity assembles transcript sequences from Illumina RNA-Seq data.
Versions and Availability
Module Names for trinity on philip
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Assemble RNA-Seq data: Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G To find out how to use these tools, type "tool -help" For example: Trinity -help #Required: # # --seqType
:type of reads: ( fa, or fq ) # # --max_memory :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc) # provied in Gb of RAM, ie. '--max_memory 10G' # # If paired reads: # --left :left reads, one or more file names (separated by commas, no spaces) # --right :right reads, one or more file names (separated by commas, no spaces) # # Or, if unpaired reads: # --single :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
Last modified: May 03 2016 07:49:54.