[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network

Kristine Briedis KBriedis at accelrys.com
Fri Jan 30 17:10:19 EST 2009


Hi Chris,

We ran our set of Pipeline Pilot nightly regressions using BioPerl-run.  The only thing we had a few problems with was HMMER.  We send Bio::Tools::Run::Hmmer filenames that are quoted because our filepaths sometimes contain curly brackets, which causes problems with some of the HMMER programs.  However, the file existence check in line 366 fails with a quoted filepath.  We're in the process of changing how we call HMMER so we don't think this will be a problem for us.  We just wanted to make you aware of it.

Other than that, we got everything running fine after a few minor changes.  Thanks again for all of your work!

Cheers,
Kristine



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Wednesday, January 28, 2009 9:14 AM
To: BioPerl List
Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network

All,

I would like to announce that the first alpha releases for BioPerl- 
run, BioPerl-db, and BioPerl-network are available.  These are  
designated as 1.005009_001, with a requirement for BioPerl 1.6 and  
higher (1.006000).

TODO:

1) All subdistributions need updates to the Changes, BUGS, AUTHORS,  
etc files.  Please make updates as needed to the main trunk (I'll  
merge them over to the relevant branch).
2) BioPerl-run TCoffee tests are failing for me, but it appears to be  
an issue with the executable (I get a bus error).  Is this  
reproducible for others?

I believe BioPerl-db (if configured correctly) and BioPerl-network  
should pass tests w/o problems.  However, I would like to gather as  
many test results as possible from BioPerl users prior to a final  
release on CPAN, particularly with BioPerl-run (I would like to make  
sure that tests for wrappers are bypassed if the executable isn't  
present or an environment variable isn't set).

The archives can be downloaded from here:

BioPerl-run:

http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2
http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz
http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip

BioPerl-db:

http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2
http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz
http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip

BioPerl-network:

http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2
http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz
http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip

SIGNATURES:

http://bioperl.org/DIST/SIGNATURES.md5

Cheers!

chris
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