User Tools

Site Tools


platanus-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

platanus-software [2014/11/14 15:45] (current)
joguya created
Line 1: Line 1:
 +====== 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
 +
 +===== Platanus/​1.2.1 =====
 +  * Version: 1.2.1
 +  * Link: http://​platanus.bio.titech.ac.jp/​platanus-assembler/​platanus-1-2-1/​
 +
 +
 +==== Usage ====
 +  * Show all versions of platanus<​code>​$ module avail platanus
 +
 +---------------------------------------------------------------------------------------------- /​etc/​modulefiles/​ilri ----------------------------------------------------------------------------------------------
 +platanus/​1.2.1
 +</​code>​
 +  * Load a specific version<​code>​$ module load platanus/​1.2.1</​code>​
 +  * Show help<​code>​$ platanus --help
 +platanus --help ​
 +
 +Platanus version: 1.2.1
 +Usage: platanus Command [options]
 +
 +Command: assemble, scaffold, gap_close
 +</​code>​
 +
 +==== Installation ====
 +  * platanus comes already compiled, so all you have to do is unzip & copy to export-apps<​code>​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/</​code>​
 +  * Create module file & push to github repo<​code>#​%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}</​code>​
 +  * Clone repo on all compute nodes using ansible<​code>​ansible-playbook compute.yml --limit=compute --tags=modules -K</​code>​
  
platanus-software.txt · Last modified: 2014/11/14 15:45 by joguya