wiki:BigCompute

Version 122 (modified by Barbera van Schaik, 12 years ago) (diff)

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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.

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

More information about data access

Data location on grid

Data

The data is located on the grid storage and only readable and writable for the vlemed/gvnl group.

Storage location (LFC resource): lfc.grid.sara.nl

Path: /grid/vlemed/gvnl/data

URI: lfn://lfc.grid.sara.nl:5010/grid/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)
  • Utrecht (Ies)
  • Rotterdam (Slavik)
  • Leiden (Jeroen)
  • Huygens (Jan)
  • Lisa
  • Philips (is one of the grid sites)
  • DAS

Grid

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