Differences

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--- tassel-software [2014/09/19 12:48] – joguya
+++ tassel-software [2024/10/22 12:53] (current) – aorth
@@ Line 1: / Line 1: @@
-===== Tassel ======
+===== tassel ======
-  * Version 3.0.165
+TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
-  * Added August, 2014
-  * Link [[http://www.maizegenetics.net/tassel/]]
-  * One of the scientist requested us to add a new module known as [[http://www.maizegenetics.net/tassel/|tassel]] for evaluating traits associations, evolutionary patterns, and linkage disequilibrium.
+===== Information =====
+  * Version: 5.2.94
+  * Added: November, 2021
+  * Updated: October, 2024
+  * Link: https://www.maizegenetics.net/tassel
-==== Usage ====
+===== Usage =====
-  * Load tassel module
+See which versions are available:
-  * <code>
-module load tassel/3.0.165
-</code>
-> **NOTE**
+<code>$ module avail tassel</code>
-> 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:<code>-Xms512m -Xmx4096m</code>
-> For example:<code>run_pipeline.pl -Xms512m -Xmx4096m</code>
+Load one version into your shell's environment and run it:
-==== Installation ====
+<code>$ module load tassel/5.2.94
-  * 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.
+$ run_pipeline.pl</code>
-  * Copy over the binaries to /export/apps/tassel/tassel_version_number/ i.e. **/export/apps/tassel/3.0.165/**
-  * Clone [[https://github.com/ilri/hpc-environment-modules|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
-  * <code>
-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/
-</code>
-  * Clone environment modules & add a new module
+**Note:** Tassel uses a default memory of ''-Xms512m -Xmx1536m'', so you will probably want to increase that so it doesn't crash, for example: ''run_pipeline.pl -Xms512m -Xmx4096m''
-  * <code>
-git clone https://github.com/ilri/hpc-environment-modules.git
-cd hpc-environment-modules/
-mkdir /
-vim tassel/3.0.165
-</code>
-  * tassel module file
+===== Sample Script =====
-  * <file>
+Sample sbatch script for running via SLURM, //tassel.sbatch//:
-#%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/"
+<file>#!/usr/bin/env bash
-# for TCL script use
+#SBATCH -p batch
-set     version         3.0.165
+#SBATCH -J tassel
-set     appname         tassel
+#SBATCH -n 10
-set     prefix          /export/apps/${appname}/${version}
-set     exec_prefix     ${prefix}
-conflict tassel
+current_date=$(date +%Y-%m-%d)
-prepend-path    PATH            ${exec_prefix}
+DATADIR="/home/monyango/data/cullicoides_br/$current_date"
-conflict tassel
+# create current_day folder
+mkdir $DATADIR
-# tassel depends on perl 5.16.3, load the perl module as well
+#create UNEAK folder in $DATADIR
-if { ![is-loaded perl] } {
+mkdir ${DATADIR}/UNEAK
-        module load perl
-}
-</file>
-  * Deploy new module using ansible
+#load tassel module
-  * <code>
-ansible-playbook site.yml -i private/hosts --limit compute --tags=modules -u joguya -K
-</code>
-  * Test to confirm success: do a module avail, module load tassel/3.0.165
-  * <code>
-module avail
 module load tassel/3.0.165
-module ls
-run_anything.pl
+#sequence keys
-module unload
+illumina_sequence_data='/home/monyango/data/cullicoides_br/Co_s_5_sequence.txt.gz'
-</code>
+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 ${DATADIR}/UNEAK -mnMAF 0.05 -mxMAF 0.5  -mnC 0 -mxC 1 -endplugin -runfork1</file>
+==== Installation =====
+Notes from the sysadmin during installation:
+<code>$ git clone https://bitbucket.org/tasseladmin/tassel-5-standalone.git -b V5.2.94
+$ cd tassel-5-standalone
+$ sudo mkdir -p /export/apps/tassel/5.2.94
+$ sudo cp -rv * /export/apps/tassel/5.2.94</code>