Groningen cluster

People UMCG: Morris, Freerk, more?

Description Description here about code template and automatic PBS script generation. Job submission/monitoring

Port applications to Dutch Life Science Grid

People

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

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

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 (currently working on the implementation). This is a pipeline to annotate variants (gene, dbsnp, hapmap, 1000g, conservation, etc)

Implemented components of the Groningen pipeline A more detailed description will follow later

• BwaIllumina (implementation phase) - pe00-bwa-align-pair1.ftl, pe01-bwa-align-pair2.ftl, pe02-bwa-sampe.ftl, pe03-sam-to-bam.ftl, pe04-sam-sort.ftl
• MarkDuplicates (implementation phase) - pe05-mark-duplicates.ftl
• PicardQC (implementation phase) - pe04b-picardQC.ftl
• ​progress WF

To be implemented

• The components of the Groningen pipeline that not implemented as a workflow component yet
• Pindel

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

Alternatives

Clusters

• Groningen
• 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