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 being 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

Pages

• Implemented workflows
• Analysis progress
• Weekly reports?

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.

Alternatives

Clusters

• Groningen (Freerk)
  • Description here about code template and automatic PBS script generation. Job submission/monitoring
• Utrecht (Ies)
• Rotterdam (Slavik)
• Leiden
• Huygens (Jan)
• Lisa
• Philips (is one of the grid sites)
• 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