Transrate 1.0.3

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)

Installation

The following procedure is the easiest way to install Transrate in a cluster.

  1. Download the binaries and unzip the file:

    $ mkdir build && cd build
$ wget https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz
$ tar -xzvf transrate-1.0.3-linux-x86_64.tar.gz

  2. Then we add the directory path to the PATH environment variable:

    $ cd transrate-1.0.3-linux-x86_64
$ export PATH=$(pwd):$PATH

  3. After, the ruby module is loaded (version 2.6.4)

    $ module load ruby/2.6.4p104_intel-19.0.4

  4. Now, we proceed to install the dependencies and the application itself:

    $ transrate --install-deps all
$ gem install transrate

  5. After the installation is completed you have to create the corresponding module for Transrate 1.0.3

    #%Module1.0#####################################################################
##
## modulefile transrate/1.0.3_ruby-2.6.4p104_intel-19.0.4
##
## Written by Hamilton Tobon Mosquera.

proc ModulesHelp { } {
    global version modroot
    puts stderr "\ttransrate - Software for de-novo transcriptome assembly \
                \n\tquality analysis.\n"
}

module-whatis "\n\n\tSets the environment for using transrate 1.0.3 ruby gem."

conflict transrate

# for Tcl script use only
set     topdir       ~/.local
set     version      1.0.3
set     sys          x86_64-redhat-linux

module load ruby/2.6.4p104_intel-19.0.4

Running Examples

This guide will take you through the basic ways of using Transrate. It’s worth reading through once even if you’re familiar with running command-line tools, as it provides guidance about proper selection of input data [1] .

Get Some Data

If you don’t have your own data, you can use our small example dataset to try out the contig and read-based metrics:

$ mkdir example && cd example
$ wget https://bintray.com/artifact/download/blahah/generic/example_data.tar.gz
$ tar -xzvf example_data.tar.gz
$ cd example_data

To continue reviewing the examples worked with this file and the functionality of transrate check the following link: http://hibberdlab.com/transrate/getting_started.html

References

[1]TransRate: reference free quality assessment of de-novo transcriptome assemblies (2016). Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly. Genome Research doi: http://dx.doi.org/10.1101/gr.196469.115

Authors