Platanus

Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples.

First, it constructs contigs using the algorithm based on de Bruijn graph.

Second, the order of contigs is determined according to paired-end (mate-pair) data and constructs scaffolds.

Finally, paired-end reads localized on gaps in scaffolds are assembled and gaps are closed.

More Info: http://platanus.bio.titech.ac.jp/platanus-assembler

Version: 1.2.1

Link: http://platanus.bio.titech.ac.jp/platanus-assembler/platanus-1-2-1/

Show all versions of platanus

$ module avail platanus

---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
platanus/1.2.1

Load a specific version

$ module load platanus/1.2.1

Show help

$ platanus --help
platanus --help 

Platanus version: 1.2.1
Usage: platanus Command [options]

Command: assemble, scaffold, gap_close

platanus comes already compiled, so all you have to do is unzip & copy to export-apps

mkdir ~/src/platanus
cd ~/src/platanus
wget http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201/platanus
chmod +x platanus
sudo mkdir -p /export/apps/platanus/1.2.1/
sudo cp platanus /export/apps/platanus/1.2.1/

Create module file & push to github repo

#%Module1.0
#####################################################################
##
## Platanus Modulefile
## By James Oguya, j.oguya@cgiar.org
## November, 2014
##

set appname         platanus
set version         1.2.1
set prefix          /export/apps/${appname}/${version}
set exec_prefix     ${prefix}
set url "http://platanus.bio.titech.ac.jp/platanus-assembler/platanus-1-2-1/"
set msg "Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples.\nPlatanus Official Site: $url\n"

module-whatis $msg

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

conflict        platanus

prepend-path    PATH    ${exec_prefix}

Clone repo on all compute nodes using ansible

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