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 (done) - pe00-bwa-align-pair1.ftl, pe01-bwa-align-pair2.ftl, pe02-bwa-sampe.ftl, pe03-sam-to-bam.ftl, pe04-sam-sort.ftl
• MarkDuplicates (done) - pe05-mark-duplicates.ftl
• PicardQC (partly done) - pe04b-picardQC.ftl. Didn't get the R environment up and running yet, so the .pdf .hist and .bamindexstats can not be produced yet. Will continue with the other components and fix this later. Attachment contains info about the required R packages.
• ReAlign (in progress) - pe06-realign.ftl

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