User Tools

Site Tools


muscle-software

Muscle

  • Version 3.8.31
  • Added August, 2014
  • One of the scientist requested us to add a new module known as muscle for amino acids alignment.
  • Download muscle binaries, in /export/apps/, create muscle/ folder & in it create muscle_version_number in this case it would be 3.8.31.
  • Copy over the binaries to /export/apps/muscle/muscle_version_number/ i.e. /export/apps/muscle/3.8.31/
  • Clone hpc-environment-modules from github
  • cd to hpc-environment-modules git repo & mkdir muscle, in it create the module file & name it the version number i.e. 3.8.31
  • Commit & push to github
  • Run ansible & limit to compute nodes & modules tag
ssh hpc
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar -xvf muscle3.8.31_i86linux64.tar.gz
sudo su -
mkdir -p /export/apps/muscle/3.8.31
cp muscle /export/apps/muscle/3.8.31/
  • Clone environment modules & add a new module
git clone https://github.com/ilri/hpc-environment-modules.git
cd hpc-environment-modules/
mkdir muscle/
vim muscle/3.8.31
  • Muscle module file
#%Module1.0#####################################################################
##
## Muscle modulefile
## By James Oguya <j.oguya@cgiar.org>
## August, 2014
##

module-whatis "muscle is a program for creating multiple alignments of amino acid or nucleotide sequences"

# for TCL script use
set     version         3.8.31
set     appname         muscle
set     prefix          /export/apps/${appname}/${version}
set     exec_prefix     ${prefix}

prepend-path    PATH            ${exec_prefix}
  • 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 muscle/3.8.31, muscle
module avail
module load muscle/3.8.31
module ls
muscle
module unload
muscle-software.txt · Last modified: 2014/08/11 16:11 by joguya