LONI | Documentation | Software

trinity

Table of Content

Version and Availability
About
Usage
Resources

Versions and Availability

Module Names for trinity on smic

Machine	Version	Module Name
smic	2.12.0	trinity/2.12.0/intel-19.0.5

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

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)
~/.profile

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 Modules. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

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.

Default Setup

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

The command

$ 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).

Managing Modules

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.

▶ Did not find the version you want to use??

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.

Types of request

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

The user's home directory

Software packages installed here will be accessible only to the user.
It is suitable for software packages that will be used by a single user.
Python, Perl and R modules should be installed here.

/project

Software packages installed in /project can be accessed by a group of users.
It is suitable for software packages that
- Need to be shared by users from the same research group, or
- are bigger than the quota on the home file syste.
This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.

/usr/local/packages

Software packages installed under /usr/local/packages can be accessed by all users.
It is suitable for software packages that will be used by users from multiple research groups.
This type of request must be sent by the PI of a research group.

How to request

Please send an email to sys-help@loni.org with the following information:

Your user name
The name of cluster where you want to use the requested software
The name, version and download link of the software
Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
Why the software is needed
Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.

About the Software

Trinity assembles transcript sequences from Illumina RNA-Seq data. - Homepage: Trinity assembles transcript sequences from Illumina RNA-Seq data.

Usage

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 )

Resources

Project page and documentation links.

Last modified: September 10 2020 11:58:50.