From heikki at nildram.co.uk Mon Dec 8 15:18:54 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Mon Dec 8 18:55:58 2003
Subject: [Bioperl-announce-l] Bioperl-run Developer snapshot 1.3.01
Message-ID: <200312082018.54358.heikki@nildram.co.uk>
Bioperl-run Developer snapshot 1.3.01
-------------------------------------
This is a developer release 1.3.01 of Bioperl-run which contains wrappers for
external programs. The stable one will be released together with bioperl core
1.4.
http://bioperl.org/DIST/current_run_unstable.tar.gz
http://bioperl.org/DIST/bioperl-run-devel-1.3.01.tar.gz
Highlights:
New wrappers for primer3 and hmmer. There is now a workflow modulue for Pise.
Critical fixes for the following wrappers: Neighbor (PHYLIP), Vista,
mfold (support for new v. 3.1.2)
Enjoy,
-Heikki
on behalf of the Bioperl core team
NEW FILES:
+ Bio::Tools::Run::Primer3
- Porting Rob Edwards extension of Primer3 wrapper and parser
+ Bio::Tools::Run::Hmmer
- Hmmer wrapper factory, currently supports hmmsearch,
hmmalign,hmmpfam, hmmbuild and hmmcalibrate
+ t/Hmmer.t
- test for Hmmer
+ Bio::Tools::Run::PiseWorkflow
- PiseWorkflow is a module for building and running a workflow on
top of PiseApplication instances.
CHANGED FILES:
* Bio::Tools::Run::Phylo::Phylip::Neighbor
- properly get the hash value
* Bio::Tools::Run::Phylo::Molphy::ProtML
- align the code
* Bio::Tools::Run::Vista
- Added java param to allow setting of java parameters, for example
to set higher heap sizes..
- Major bug, need to project aligmnents, basically need to remove
position in pairwise aligmnet if both are gap characters, else
vista will count wrongly
* Bio::Tools::Run::Alignment::Lagan
- Allowing of setting of outfile
- can't declare and expect a variable at the same time
* Bio::Tools::Run::FootPrinter
- fix stupidity with tempfilehandle and outfh not being closed
properly as reported by Ben Westover
* Bio::Tools::Run::EMBOSSApplication
- no need for this debugging
* Bio::Tools::Run::PiseApplication::mfold
- Pise/bioperl module for a recent version of mfold (3.1.2).
* Bio::Tools::Run::Phylo::Phylip::Consense
- typo
* Bio::Tools::Run::Phylo::PAML::Codeml
- fix typo reported in bug #1505
- default should be an arrayref
- George Hartzell fixes
* Bio::Tools::Run::Phylo::PAML::Yn00
- bug #1507, SYNOPSIS is runnable now with API changes
- bug #1507 add MSwin .exe extension where appropriate
- wait -this isn't necessary , we already pad the PROGRAMNAME with
the .exe when appropriate
- George Hartzell fixes
* Bio::Tools::Run::FootPrinter
- POD fixes
* Bio::Tools::Run::Alignment::Blat
- well, at least it runs the blat program now, although it isn't
seemingly able to find the output tempfile to retrieve the results
* t/Blat.t
- well, at least it runs the blat program now, although it isn't
seemingly able to find the output tempfile to retrieve the results
- various fixes to get blat runnable in line with bioperl-live 1.2.3
all tests now pass.
* t/Mdust.t
- typo
* Bio::Tools::Run::Mdust
- use save_tempfiles, use PROGRAMNAME as a variable, use tempfile
instead of randomly generating filename
- Modified call to io->tmpfile to get file name as well as handle
* Makefile.PL
- George Hartzell fixes
* scripts/panalysis.PLS
- Patched, thank you Albert
* AUTHORS
- updated using info from maintanence/authors.pl script
From heikki at nildram.co.uk Mon Dec 8 15:18:37 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Mon Dec 8 18:55:59 2003
Subject: [Bioperl-announce-l] Bioperl-ext Developer snapshot 1.3.01
Message-ID: <200312082018.37975.heikki@nildram.co.uk>
Bioperl-ext Developer snapshot 1.3.01
-------------------------------------
This is a developer release 1.3.01 of Bioperl-Ext which contains C compiled
Extensions. The stable one will be released together with bioperl core 1.4.
http://bioperl.org/DIST/current_ext_unstable.tar.gz
http://bioperl.org/DIST/bioperl-ext-devel-1.3.01.tar.gz
Changes since 0.6
-----------------
Yee Man Chan's has written alternative pairwise alignment code into
Bio/Ext/Align which is accessed by Bio::Tools::dpAlign in
bioperl-live. Read the README for details
Enjoy,
-Heikki
on behalf of the Bioperl core team
NEW FILES
=========
* Bio/Ext/Align/libs/{dpalign.c dpalign.h linspc.c}
incorporate Yee Man Chan's alternative alignment code
CHANGES
=======
* README
updated to include info about dpAlign and common io_lib problems
* Bio::Ext::Align {Align.xs Makefile.PL typemap}
incorporate Yee Man Chan's alternative alignment code
From heikki at nildram.co.uk Wed Dec 17 18:28:59 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Thu Dec 18 07:52:19 2003
Subject: [Bioperl-announce-l] Bioperl Developer snapshot 1.3.04
Message-ID: <200312172328.59980.heikki@nildram.co.uk>
Bioperl Developer snapshot 1.3.04
----------------------------------
This is the fourth and last developer snapshot from the BioPerl CVS
head before release 1.4 which is due early next week. Bug fixes are
still welcome, but please do not commit anything you do not have
time to test well.
http://bioperl.org/DIST/current_core_unstable.tar.gz
http://bioperl.org/DIST/bioperl-1.3.04.tar.gz
Changes since 1.3.04
--------------------
This time I dit not have the time to collect details from all the cvs
commits (maybe that level of detail is not necessary? It is all in
bioperl-guts, anyway.) The highlights are:
* SVG::Graphics fine tuning ; SVG output,
* Bio::Tree major changes plus a new howto. There is a new
Feature-Annotation howto, too.
* Parse more BLAST statistics and lots of BLAST-related fixes
* Bio::Restriction::Analysis is now fixed and can handle overlapping
and multiple cuts as well as circular sequences.
* Bio::SearchIO and Bio::AlignIO can quess the incoming format by
looking ahead into stream, thanks to Bio::Tools::GuessSeqFormat.
* GenBank and EMBL parsers now tolerate words longer than line
width. Also, they parse non-binomial virus names better into
Bio::Species objects. EMBL parser now does better roundtrip of
files.
* New GAME format modules.
* last minute fix: scripts/Bio-DB-GFF/bp_genbank2gff.PLS can now write
to stdout without depending on mysql.
NEW FILES:
* Bio/OntologyIO/Handlers::InterPro_BioSQL_Handler.pm
* Bio/Restriction/IO::bairoch.pm
* Bio/SeqIO::game.pm
* Bio::Tools::GuessSeqFormat
* doc/howto/sgmlFeature-Annotation.sgml
* doc/howto/sgm/Trees.sgml
* examples/biographics/all_glyphs.pl
Enjoy,
-Heikki & the rest of the bioperl core team
P.S. The web site was updated over five hours ago when I wrote the
first version of this message which seems to have vanished into a black
hole,
--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________
From heikki at nildram.co.uk Tue Dec 23 04:11:35 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Tue Dec 23 10:49:49 2003
Subject: [Bioperl-announce-l] Bioperl Release 1.4
Message-ID: <200312230911.35200.heikki@nildram.co.uk>
Bioperl Release 1.4
--------------------
The stable Bioperl release 1.4 is available for immediate use at:
http://bioperl.org/DIST
We are releasing simultaneously three modules:
bioperl-core - core bioperl modules
http://bioperl.org/DIST/current_core_stable.tar.gz
http://bioperl.org/DIST/current_core_stable.tar.bz2
bioperl-ext - C compiled extensions
http://bioperl.org/DIST/current_ext_stable.tar.gz
http://bioperl.org/DIST/current_ext_stable.tar.bz2
bioperl-run - wrappers for external programs
http://bioperl.org/DIST/current_run_stable.tar.gz
http://bioperl.org/DIST/current_run_stable.tar.bz2
They will also appear shortly at IUBIO mirror
(later today)
and in CPAN .
Remember, all the external modules needed by bioperl-core can be
installed from CPAN under name Bundle-BioPerl
.
Changes
-------
Over 3000 file changes have gone into this release since the 1.2
development tree was branched off from the main. These are the
main feature enhancements:
o installable scripts
o global module version from Bio::Root:Version
o Bio::Graphics - major improvements; added SVG support
o Bio::Popgen - population genetics
o Bio::Restriction - new restrion analysis modulues
o Bio::Tools::Analysis - web based DNA and Protein analysis
framework and several implementaions
o Bio::Seq::Meta - per residue annotable sequences
o Bio::Matrix
o Bio::Matrix::PSM - Position Scoring Matrix
o Bio::Ontology - major contributions
o Bio:Tree
o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA
o Bio::SeqFeature::Tools - seqFeature mapping tools,
e.g. Bio::SeqFeature::Tools::Unflattener.pm
o Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment
(needs Bioperl-ext)
o new Bio::SearchIO formats
o new Bio::SeqIO formats: tab, kegg, tigr, game; important fixes for
old modulues
o Bio::AlignIO: maf
o improved Bio::Tools::Genewise
o Bio::SeqIO now can recognize sequence formats automatically from stream
o new parsers in Bio::Tools:
Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
o several new HOWTOs: SimpleWebAnalysis, Trees, Feature Annotation,
OBDA Access, Flat Databases
o hundreds of new and improved files
For detailed documentation, see individual module documentation in the
distribution or in http://doc.bioperl.org/. The tutorials are
available at http://bioperl.org/HOWTOs/.
This release is a result of hard work by the bioperl core team, nearly
hundred developers and countless suggestions and bug reports at the
bioperl mailing list (bioperl-l@bioperl.org) or the the bioperl bug
tracking system (http://bugzilla.bioperl.org/).
Wishing you all Peaceful Christmas,
-Heikki and all the bioperl developers