• TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
• Link: http://ccb.jhu.edu/software/tophat/

• show available versions:

  $ module avail tophat2
  
  ---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
  tophat2/2.0.11 tophat2/2.0.13 tophat2/2.0.3  tophat2/2.0.8b

• load v2.0.13:

  $ module load tophat2/2.0.13

• show help info:

  $ tophat2 --help

NOTE
Older versions of tophat2 required SAMtools to be loaded/present, unlike this new version which comes with its own SAMtools inorder to avoid incompatibility issues.

*

wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz
tar -xvf tophat-2.0.13.Linux_x86_64.tar.gz
sudo mkdir /export/apps/tophat2/2.0.13
cp -rv tophat-2.0.13.Linux_x86_64/* /export/apps/tophat2/2.0.1

• create module file:

  #%Module1.0
  #####################################################################
  ##
  ## tophat Modulefile
  ## by James Oguya, <j.oguya@cgiar.org>
  ## October, 2014
  ##
  
  set appname         tophat2
  set version         2.0.13
  set prefix          /export/apps/${appname}/${version}
  set exec_prefix     ${prefix}
  set url "http://tophat.cbcb.umd.edu"
  set msg "TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.\nTophat2 Official Site: $url\n"
  
  proc ModulesHelp { } {
      puts stderr "$msg"
  }
  
  module-whatis   "$msg"
  
  conflict tophat tophat2
  
  prepend-path    PATH        ${exec_prefix}
  
  # tophat v2.0.13 removed SAMtools as an external dependency in order to avoid incompatibility issues with recent and future changes of SAMtools and its code library (an older, stable SAMtools version is now packaged with TopHat)

• deploy using ansible

  ansible-playbook compute.yml --limit=compute --tags=modules -K