trinity

About

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Versions and Availability

▶ Display Softenv Keys for trinity on all clusters
Machine Version Softenv Key
None Available N/A N/A
▶ Softenv FAQ?

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

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft
▶ Display Module Names for trinity on all clusters.
Machine Version Module
philip 2.1.0 trinity/2.1.0/INTEL-15.0.3
▶ **FIX-ME** FAQ?

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

Last modified: May 03 2016 07:49:54.