http://bioinformatics.ubc.ca/pegasys/
Dear potential Pegasys users.
We are pleased to announce the release of version 0.5 of the
Pegasys client and server software packages.
Pegasys is a software for executing and integrating analyses
of biological sequences. It was published in BMC Bioinformatics
last fall. This is the first announced released since the
publication. (publication is linked to in URL above)
Graham McVicker, software developer at UBiC, has led
the Pegasys development group over the last 6 months and
has coordinated a number of changes that represent the
culmination of work to improve the overall stability
and scalability of the Pegasys software system.
Future work on the Pegasys project will leverage
these improvements to provide additional features
and a broader suite of integrated analysis programs.
Version 0.5 of the server and the client binaries and source
code are now available for download from the Pegasys download
page:
http://bioinformatics.ubc.ca/pegasys/downloads/
Pegasys is distributed under the OSI banner.
http://opensource.org/docs/certification_mark.php
Precompiled client binaries are currently available for
Linux x86 (tested against Mandrake 10), Mac OS X, and
Windows (tested against Windows XP).
Note that version o.5 of the Pegasys client are *not*
compatible with versions of the Pegasys server before 0.5,
and you therefore download both clients and servers
version 0.5.
The documentation has also been updated:
http://bioinformatics.ubc.ca/pegasys/docs/
The following is a summary of the changes made to the
Pegasys server and client code:
--------------------
Server Code changes
--------------------
- A more modular and structured database access API.
- Reduced dependencies on NFS.
- Improved error handling.
- No longer necessary to manually load database reagents
and evidence types before server start up. Now loaded
automatically by server when required.
- Notification to client of job failure.
- Automatic resubmission of failed or timed-out jobs.
- Large reduction in the number threads used by the server.
- More communication of status from running jobs back to server.
- Decentralised database storing and result parsing performed
by running jobs rather than by server.
- Ability to halt a running DAG.
- Automated cleanup of temporary files created by the server,
queuing system and analysis programs.
- Many bug fixes, documented in source code.
--------------------
Client Code changes
--------------------
- Stop DAG button now halts running workflow on server side.
- Failed job status and error messages now displayed in client.
- Connection with server now validated through handshake.
- Many bug fixes and usability improvements, documented in
source code.
-------------------------------------------------------------
For further information please contact the information
desk at UBiC:
http://bioinformatics.ubc.ca/pegasys/contact/
Subscribe to the Pegasys-announce mailman managed
list, at:
http://perutz.cmmt.ubc.ca/mailman/bioinformatics.ubc.ca/listinfo/pegasys-announce
or e-mail us at info at bioinformatics.ubc.ca
cheers to all,
francis, on behalf of the current Pegasys development team:
Graham McVicker
Jessica Sawkins
Mack Yuen
Francis Ouellette
--
BF Francis Ouellette http://bioinformatics.ubc.ca/ouellette
---
