Cassava Production Pipeline¶

Terry Casstevens (tmc46@cornell.edu)

May 15, 2014

Requirements¶

Must have git installed. Check using this command... git ----version

Must have Java 7 installed. Check using this command... java --version

To Initially Download Tassel 5 Standalone Code...¶

git clone https://github.com/maize-genetics/tassel.git

To Update Packages to Latest Source Code...¶

git pull

Example Configuration File...¶

/home/tmc46/CassavaProdPipeline/rawSeqs/

/home/tmc46/CassavaProdPipeline/inputFiles/keyfile.txt
ApeKI
/export/species/Manihot_esculenta/gbs/topm/productionTOPM_T5_20140327.topm
/home/tmc46/CassavaProdPipeline/genotypes/CassavaGenotypes.h5

/home/tmc46/CassavaProdPipeline/archive/

Description of Configuration File Parameters...¶

Usage:

ProductionPipeline

--inputDirectory : Input directory containing fastq AND/OR qseq files (required)

--keyFile : Barcode Key File (required)
--enzyme : Enzyme used to create the GBS library (required)

--productionTOPM : Physical map file containing tags and corresponding variants (production TOPM) (required)

--outputGenotypeFile : Output (target) HDF5 genotypes file to add new genotypes to (new file created if it doesn't exist) (required) --archiveDirectory : Archive directory where to move processed files (required)

To Execute Pipeline…¶

First symbolic link raw sequence files into rawSeqs directory…¶

ln --s

/export/species/Manihot_esculenta/gbs/fastq/fastq1/c14cgacxx_7_fastq.txt.gz /home/tmc46/CassavaProdPipeline/rawSeqs/

Then execute the pipeline with this command…¶

/home/tmc46/tassel--5--standalone/run_pipeline.pl --Xmx10g --configFile /home/tmc46/CassavaProdPipeline/inputFiles/CassavaProdPipeline.xml

Cron Job (i.e. Execute at 2:30 a.m. every day)¶

30 2 * * * root /home/tmc46/tassel--5--standalone/run_pipeline.pl --Xmx10g

--configFile /home/tmc46/CassavaProdPipeline/inputFiles/CassavaProdPipeline.xml