wiki:BigCompute

Analysis on the Dutch Life Science Grid

People

  • UMCG: Freerk van Dijk, Morris Swertz
  • AMC: Barbera van Schaik, Mark Santcroos, Silvia D Olabarriaga, Antoine van Kampen
  • LUMC/TU Delft: Jan Bot, Kai Ye
  • Sara/BiGGrid: Tom Visser

Data location

Data is stored within the bbmri.nl virtual organisation (VO).

Workflow location

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.

Available systems

  • Groningen (Freerk)
  • Grid (Barbera, Jan)
  • Utrecht (Ies)
  • Rotterdam (Slavik)
  • Leiden (Jeroen)
  • Huygens (Jan)
  • Lisa
  • Philips (is one of the grid sites)
  • DAS
  • Cloud

Reading material e-BioInfra

Reading material ToPiCas

  • ADD REFERENCES HERE
Last modified 6 years ago Last modified on Jul 3, 2011 1:56:12 PM

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