ILRI Research Computing

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====== TransDecoder ======
  * TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

==== v2.0.1 ====
  * Version: 2.0.1
  * Added: February, 2015
  * Link: http://transdecoder.github.io/

=== Usage ===
  * Show all available versions of TransDecoder<code>module avail TransDecoder</code>
  * Load TransDecoder module: <code>module load TransDecoder/2.0.1</code>

=== Installation ===
  * clone TransDecoder repo & compile it<code>git clone git@github.com:TransDecoder/TransDecoder.git
git checkout 2.0.1
make
sudo mkdir -p /export/apps/TransDecoder/2.0.1/
sudo cp -r . /export/apps/TransDecoder/2.0.1/
</code>
  * TransDecoder module file<code>
#%Module1.0
#####################################################################
##
## TransDecoder Modulefile
## By James Oguya, j.oguya@cgiar.org
## February, 2015
##

set appname             TransDecoder
set version             2.0.1
set prefix              /export/apps/${appname}/${version}
set exec_prefix_util    ${prefix}/util
set exec_prefix_bin     ${exec_prefix_util}/bin

set url "http://transdecoder.github.io/"
set msg "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.\nTransDecoder Official Site: $url\n"

module-whatis $msg

proc ModulesHelp { } {
    puts stderr "$msg"
}

conflict        TransDecoder

prepend-path    PATH    ${prefix}
prepend-path    PATH    ${exec_prefix_util}
prepend-path    PATH    ${exec_prefix_bin}</code>

  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules</code>