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

Chris Fields cjfields at illinois.edu
Fri Jan 30 17:29:18 EST 2009


np.  Let me know if anything else pops up.

chris

On Jan 30, 2009, at 4:10 PM, Kristine Briedis wrote:

> 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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