Port applications to Dutch Life Science Grid

People

• AMC: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos
• Sara/BiGGrid: Tom Visser
• UMCG: Morris Swertz, Freerk van Dijk

Description

Software is going to be implemented as workflow components. The workflows will run on the Dutch life science grid.

• Information about the infrastructure: ​http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/
• Getting started: ​http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GettingStarted
• Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga (2010) Initial steps towards a production platform for DNA sequence analysis on the grid. BMC Bioinformatics 11: 1. Dec ​pubmed

Implemented workflow components at AMC

This list of workflow components are already available. We can expand it with Pindel and (parts of) the GATK pipeline.

• Splitting of fastq files
• Building a BWA index on the genome sequence (base space and color space)
• BWA for shotgun reads (base space and color space) It is possible to do parameter sweeps. Output is in bam format
• Merge bam results
• Samtools pileup
• Varscan (pileup to snp, indel and cns)
• Bam2coverage creates a UCSC wiggle file to display the genome coverage (per 50kbp)
• Coverage-per-base determines the coverage for every base in the genome and it summarizes the results (coverage versus frequency)
• Annovar (works for hg18, working on other assemblies). This is a pipeline to annotate variants (gene, dbsnp, hapmap, 1000g, conservation, etc)
• FastqC

Implemented components of the Groningen pipeline

Template (grid component)

Alignment, realignment, recalibration, stats

• pe0--fastqc.ftl (FastqToFastQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/quality/Workflow/FastqToFastQC.gwendia)
• pe00-bwa-align-pair1.ftl (BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
• pe01-bwa-align-pair2.ftl (BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
• pe02-bwa-sampe.ftl (BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
• pe03-sam-to-bam.ftl (BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
• pe04a-HsMetrics.ftl (CalculateHsMetrics, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/CalculateHsMetrics.gwendia)
• pe04b-picardQC.ftl (PicardQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/PicardQC.gwendia)
• pe04-sam-sort.ftl (SamSort, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/SamSort.gwendia)
• pe05-mark-duplicates.ftl (MarkDuplicates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/MarkDuplicates.gwendia)
• pe06-realign.ftl (ReAlign, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/ReAlign.gwendia)
• pe07-fixmates.ftl (FixMates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/FixMates.gwendia)
• pe08-covariates-before.ftl (GatkCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkCovariates.gwendia)
• pe09-recalibrate.ftl (GatkRecalibrate, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkRecalibrate.gwendia)
• pe10-sam-sort.ftl (SamSort, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/SamSort.gwendia)
• pe11-covariates-after.ftl (GatkCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkCovariates.gwendia)
• pe12-analyze-covariates.ftl (GatkAnalyzeCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkAnalyzeCovariates.gwendia)

Merge bam per sample and perform SNP and indel calling

• vc00a-unified-genotyper.ftl to do
• vc00b-variant-filtration.ftl to do
• vc00c-variant-eval.ftl to do
• vc00d-picardMetrics.ftl (PicardQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/PicardQC.gwendia)
• vc00-merge.ftl to do
• vc00.merge.ftl to do
• vc01-coverage.ftl to do
• vc01.unified_genotyper.ftl to do
• vc02.picardQC.ftl (PicardQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/PicardQC.gwendia)
• vc02-realigner-target-creator.ftl to do
• vc03.coverage.ftl to do
• vc03-realign.ftl (ReAlign, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/ReAlign.gwendia)
• vc04-fixmates.ftl (FixMates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/FixMates.gwendia)
• vc05-indel-genotyper-v2.ftl to do
• vc06-filter-indels.ftl to do
• vc07-unified-genotyper.ftl to do
• vc08-make-indel-mask.ftl to do
• vc09-variant-filtration.ftl to do
• vc10-variant-eval.ftl to do
• vc11-name-sort-bam.ftl (SamSort, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/SamSort.gwendia)
• Pindel (Pindel, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/pindel/Workflows/Pindel.gwendia)

Data access rights

To ensure that the most limited group of people has access to the data we have created a subgroup "gvnl" within the "vlemed" Virtual Organisation (VO). For people to become part of this group, it is required that they have a Grid certificate and that they are part of the "vlemed" VO. On the following page there is information on how to get a certificate, how to get into the "vlemed" VO: ​http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/EBioInfra#Access

For more information about data access see ​http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/DataManagement

Things to address

• Available disk space on the grid storage elements / worker nodes

Data location on grid

Data

The data is located on the storage element at Sara and only readable and writable for the vlemed/gvnl group. This screencast demonstrates how to access the data from the Vbrowser: ​http://www.youtube.com/watch?v=FicwWGAbubQ

Storage location (resource): srm.grid.sara.nl

Path: /pnfs/grid.sara.nl/data/vlemed/gvnl

Workflows and databases

These directories are open to all members of the vlemed VO

• Workflows: lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF
• Databases: lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_DB

The directories that contain the workflows have the following structure:

Directory	Description
bin	dependent binaries like bwa, samtools
GasW	component description, describes which executable has to run on grid and it specifies the in and output files/parameters
Java	dependent jar files, e.g. the GATK jar
parameterFiles	text files that contain exactly one line with the parameters that you would like to provide to bwa or another component
Scufl	old workflow description files, can be ignored
shFiles	these files are executed on the grid and described by the GASW descriptor, the gvnl shFiles are based on the Groningen templates
Workflows	Workflow descriptions, clicking on them will start the Moteur plugin. Input files/parameters can be specified in the fields. If you click on "Run" the jobs are submitted to the grid

The shell files can (in most cases) run on any linux cluster. In that case you need to place the shell file and the dependent executable(s) in one directory. At the start of each shell file is an example on how to run them.

Workflow execution

#	Sample	WF	Status	Start
1	A4a	​F ​F ​F ​workflow-425d9ceb	done
2	Vartest	​workflow-490b15f8	done
3	Iteration test	​workflow-bf48aff1	failed
4	Iteration test	​workflow-923c6588	done
5	60-samples-batch (15 lanes)	​workflow-d80b5767	10 / 15 done	11-02-2011 19:30
6	60-samples-batch A (55 lanes)	​workflow-cbaca6e5	15 / 55 done	12-02-2011 13:55
7	60-samples-batch A remaining 1 (17 lanes)	​workflow-835250b1	failed (grid very busy)	07-03-2011 17:45
8	60-samples-batch A remaining 1 (17 lanes)	​workflow-31eb952d	1/17 done	08-03-2011 14:15
9	60-samples-batch A remaining (27 lanes)	​workflow-fd98c7c8	running	15-03-2011 10:45
10	60-samples-batch G (27/54 lanes)	​workflow-a781209c	running	15-03-2011 20:37
11 | second-batch R10-11-12 (27 lanes)	​workflow-6fe1cb10	running	16-03-2011 10:57
x	60-samples-batch G (54 lanes)
x	60-samples-batch R (60 lanes)

Alternatives

Clusters

• Groningen
  • Description here about code template and automatic PBS script generation. Job submission/monitoring
• Leiden
• Huygens
• Lisa
• Philips
• DAS

Grid

• EBioInfra ​http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/
• BiGGrid Cloud ​http://www.cloud.sara.nl/
• Topos ​https://grid.sara.nl/wiki/index.php/Using_the_Grid/ToPoS