Enabling BioGrid

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Added by Olli Tourunen, last edited by Olli Tourunen on Oct 29, 2008  (view change)

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Overview

Enabling BioGrid on your resource consists of installing BioGrid supported software and authorising users in BioGrid VO. The following document covers both steps. The intended audience is
a) users looking for a list of supported software and its descriptions
b) system administrators supporting BioGrid VO.

Supported software

BioGrid supports several widely used software packages. These are made available in the grid as NorduGrid ARC Runtime Environments (REs). Here is a non-prioritized list of the REs with links to the descriptions.

BLAST

Current version: 2.2.18
URL: https://extras.csc.fi/mgrid/blast_re/

CLUSTALW

Current version: 2.0.9
URL: https://extras.csc.fi/mgrid/clustalw_re/

HMMER

Current version:2.3.2
URL: https://extras.csc.fi/mgrid/hmmer_re/

MAFFT

Current version: 6.603
URL: https://extras.csc.fi/mgrid/mafft_re/

MUSCLE

Current version: 3.7
URL: https://extras.csc.fi/mgrid/muscle_re/

Enabling BioGrid on your resource

Note to sysadmins using SGAS for accounting

Currently SGAS takes the number of threads for the job from the user's job specification. However, if the runtime environment sets the number of threads this is not directly visible to SGAS (or ARC).

For now, sites using SGAS for accounting are suggested to configure the REs to use just one core. We are working on a solution.

Installing the REs

Each RE description comes with brief installation instructions and links to the software home page. Example ARC RE-scripts are also provided. Suggested procedure:

  • pick one RE to start with (HMMER is a safe bet, possibly configured to use just one thread)
  • install it
  • authorize the VO (see below)
  • mail olli.tourunen@csc.fi to get it tested
  • continue to add more REs

If you have any questions/corrections/suggestions, please do not hesitate to mail olli.tourunen@csc.fi. These instructions are a work in progress an there is much room for improvement. With your help we can make the world a better place for other administrators running BioGrid resources.

Authorizing BioGrid VO

To authorize the BioGrid VO in your ARC cluster, you need to include the BioGrid users from the NDGF VOMS. Here is an example authorization block for arc.conf (or nordugridmap.conf if using a separate file).

[vo]
id="vo_ndgf_biogrid"
vo="ndgf_biogrid"
file="/etc/grid-security/grid-mapfile"
source="vomss://voms.ndgf.org:8443/voms/bio.ndgf.org"
mapped_unixid="suitable_account_here"

Other considerations

BioGrid will make use of NDGF's dCache storage system for accessing the common sequence databases and relies on ARC input file caching for efficiency. Check that the caching is enabled in arc.conf.