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Table of Contents
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)
- Utrecht (Ies)
- Rotterdam (Slavik)
- Leiden (Jeroen)
- Huygens (Jan)
- Lisa
- Philips (is one of the grid sites)
- DAS
eScience related links
Reading material e-BioInfra
- Information about the infrastructure
- Getting started with workflows
- 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
Reading material ToPiCas
- ADD REFERENCES HERE
Attachments (3)
-
r-environment.txt (134 bytes) - added by 14 years ago.
info about R packages
- log-picardqc-20101220.ods (17.1 KB) - added by 14 years ago.
- log-fastqc20110423.xls (118.0 KB) - added by 14 years ago.
Download all attachments as: .zip
