Bioinformatics Wrappers

This page describes two software tools, that facilitate parallelization of common bioinformatics applications on UNIX clusters.

WRAPID:
Particularly suited for cases where the whole application (including program, queries, and database) can fit into the memory space of a single node. Successfully tested with BLAST, FASTA, SSEARCH, MPSEARCH, CLUSTALW!
BLAST.pm for MOLLUSC:
If you have a large database that exceeds the RAM on your clients, use the BLAST.pm module in combination with MOLLUSC.

The main aim of their development was to make it easy - even for non-system administrators - to "harness the power of a network of computers".
More information can be found in the Readme and in the following publication:

Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, and Daniel R. Caffrey
Wrapping up BLAST and other applications for use on Unix clusters
Bioinformatics 2003 19: 441-442. [Abstract] [Print PDF]

Downloads

Get the whole package as a gzip'ed tar archive: 255 KB or access each file individually from a directory.

Updates

Feb 17th, 2003:	Wrapid: Fixed double home-directory (~/~/) and bug that caused all clients to be regarded localhosts
Feb 19th, 2003:	Wrapid: with --nice=-1 the nice call can be suppressed; fixed problem with explicit '--outdir'; added more stats to log messages

Contacts

WRAPID: Karsten Hokamp, karsten_hokamp@sfu.ca
BLAST.pm: Daniel Caffrey, daniel_r_caffrey@cambridge.pfizer.com

This site is hosted by Ken Wolfe's lab where WRAPID was developed, tested and used.

Last modified on Feb 19th, 2003.