ILRI Research Computing

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Tassel

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

Usage

Load tassel module
```
module load tassel/3.0.165
```

Memory Usage/Settings

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 set the maximum memory size to 4GB:
```
-Xms512m -Xmx4096m
```
For example:
```
run_pipeline.pl -Xms512m -Xmx4096m
```

Installation

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

Sample script written by Maria Onyango

#!/bin/env bash

#SBATCH -p batch
#SBATCH -J tassel
#SBATCH -n 10

current_date=$(date +%b_%d)

DATADIR="/home/monyango/data/cullicoides_br/$current_date"

# create current_day folder
mkdir $DATADIR

#create UNEAK folder in $DATADIR
mkdir ${DATADIR}/UNEAK

#load tassel module
module load tassel/3.0.165

#sequence keys
illumina_sequence_data='/home/monyango/data/cullicoides_br/Co_s_5_sequence.txt.gz'
gbs_barcode_keys='/home/monyango/data/cullicoides_br/GBS_barcode_key.txt'

# step 1: create workingdirplugin - create several folders in DATADIR/UNEAK
run_pipeline.pl -Xmx4096m -fork1 -UCreatWorkingDirPlugin -w ${DATADIR}/UNEAK -endPlugin -runfork1

# copy sequence data to DATADIR/UNEAK/Illumina & key to DATADIR/UNEAK/key
cp ${illumina_sequence_data} ${DATADIR}/UNEAK/Illumina/
cp ${gbs_barcode_keys} ${DATADIR}/UNEAK/key/

# step 2: derive tagcount list
run_pipeline.pl -Xmx4096m -fork1 -UFastqToTagCountPlugin -w ${DATADIR}/UNEAK -e PstI -endplugin -runfork1

# step 3: merge tag count files of the same taxon
run_pipeline.pl -Xmx4096m -fork1 -UMergeTaxaTagCountPlugin -w ${DATADIR}/UNEAK -c 5 -endplugin -runfork1

# step 4: identify tag pairs for snip calling
run_pipeline.pl -Xmx4096m -fork1 -UTagCountToTagPairPlugin -w ${DATADIR}/UNEAK -e 0.03 -endplugin -runfork1

# step 5: generate tags by taxa file
run_pipeline.pl -Xmx4096m -fork1 -UTagPairToTBTPlugin -w ${DATADIR}/UNEAK -endplugin -runfork1

# step 6: generate map info file
run_pipeline.pl -Xmx4096m -fork1 -UTBTToMapInfoPlugin -w ${DATADIR}/UNEAK -endplugin -runfork1

# step 7: output hapmap file
run_pipeline.pl -Xmx4096m -fork1 -UMapInfoToHapMapPlugin -w ${DATADIR}/UNEAK -mnMAF 0.05 -mxMAF 0.5  -mnC 0 -mxC 1 -endplugin -runfork1

Table of Contents

Tassel

Usage

Memory Usage/Settings

Installation