ILRI Research Computing

• Version 3.0.165
• Added August, 2014
• Link http://www.maizegenetics.net/tassel/
• One of the scientist requested us to add a new module known as tassel for evaluating traits associations, evolutionary patterns, and linkage disequilibrium.

• Load tassel module

• module load tassel/3.0.165

NOTE
Tassel uses java with a default memory setting of: -Xms512m -Xmx1536m
So you have to increase the maximum memory(-Xmx) to atleast 4GB otherwise tassel would run out of memory really fast
Use the following options to use custom memory setting:

-Xms512m -Xmx4096m

For example:

run_pipeline.pl -Xms512m -Xmx4096m

• Download/clone tassel repo, in /export/apps/, create tassel/ folder & in it create tassel_version_number folder in this case it would be 3.0.165.
• Copy over the binaries to /export/apps/tassel/tassel_version_number/ i.e. /export/apps/tassel/3.0.165/
• Clone hpc-environment-modules from github
• cd to hpc-environment-modules git repo & mkdir tassel, in it create the module file & name it the version number i.e. 3.0.165
• Commit & push to github
• Run ansible & limit to compute nodes & modules tag

• ssh hpc
  git clone git://git.code.sf.net/p/tassel/tassel3-standalone tassel3
  cd tassel3/
  git checkout V3.0.165
  sudo su -
  mkdir -p /export/apps/tassel/3.0.165/
  cp -rv * /export/apps/tassel/3.0.165/

• Clone environment modules & add a new module

• git clone https://github.com/ilri/hpc-environment-modules.git
  cd hpc-environment-modules/
  mkdir /
  vim tassel/3.0.165

• tassel module file

• #%Module1.0#####################################################################
  ##
  ## tassel modulefile
  ## By James Oguya <j.oguya@cgiar.org>
  ## August, 2014
  ##
  
  module-whatis "Tassel is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. http://www.maizegenetics.net/tassel/"
  
  # for TCL script use
  set     version         3.0.165
  set     appname         tassel
  set     prefix          /export/apps/${appname}/${version}
  set     exec_prefix     ${prefix}
  
  conflict tassel
  
  prepend-path    PATH            ${exec_prefix}
  
  conflict tassel
  
  # tassel depends on perl 5.16.3, load the perl module as well
  if { ![is-loaded perl] } {
          module load perl
  }

• Deploy new module using ansible

• ansible-playbook site.yml -i private/hosts --limit compute --tags=modules -u joguya -K

• Test to confirm success: do a module avail, module load tassel/3.0.165

• module avail
  module load tassel/3.0.165
  module ls
  run_anything.pl
  module unload