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Kai Blin | 3 Jul 2010 09:05
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Re: Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0)

On Fri, 2010-07-02 at 10:46 -0500, Chris Fields wrote:

Hi Chris,

> > As for the ubuntu platform a simple command like: "sudo apt-get
> > install bioperl" simply does the trick!
> > However I couldn't find this simple command in your installation
> > guidelines, and I don't really understand why I should set up a
> > server, before installing bioperl and then follow this complicated
> > series of instructions, to achieve something that is so simple!
> 
> That's b/c the bioperl that is installed with apt is not up to date.
> CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for
> bioperl-run (where CPAN is at v.1.6.1).  

As Steffen already said, the current Ubuntu version is 1.6.1, for both
bioperl and bioperl-run. I don't think providing backports for
Debian/Ubuntu versions wouldn't be too hard.

> I would like to get the releases to a point where they are easily
> packaged for apt/yum/ppm/fink/macports/whatever, so any help along
> those lines is greatly appreciated.

There currently is only an "automated port" of Bioperl on the openSuse
Build Service (OBS). I'll probably end up looking into packaging BioPerl
for SLES11, and would do that on OBS. Supporting other suse distros is
trivial, other RPM-based distros are doable once you figure out the
package names.

I'd say if Debian, Fedora, Suse and Ubuntu are covered, you're doing
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Christopher Bottoms | 3 Jul 2010 17:30
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Fwd: Codefest 2010: Final details

 I will be there first thing Wednesday morning. I'd be glad to help work on
any project.

On Sat, Jul 3, 2010 at 9:15 AM, Chris Fields <cjfields <at> illinois.edu> wrote:

> I will be there on the afternoon of the 7th.  There are a couple of
> projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I
> think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not
> sure where that is (might be surplanted by SQLite work?).  Would be nice to
> talk with Mark re: the wrapper system for BioPerl as well.
>
> So lots of stuff to think over and plan for.  Maybe we should move this to
> open-bio-l, or bioperl-l?
>
> chris (fields)
>
> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>
> > Chris,
> >
> > I do not have too much experience on cloud computing, either. There
> > will be quite a few people from BioPerl . We'll meet and  come up with
> > a plan first thing in the morning. Unless someone has a very good one
> > ready for sharing...
> >
> >     -Heikki
> >
> > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> > cell: +966 545 595 849  office: +966 2 808 2429
> >
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Chris Fields | 3 Jul 2010 20:23
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Re: Error when Using BLAT????

On Jun 29, 2010, at 8:58 AM, Minh Bui wrote:

> Hi everyone,
> I am writing an application that allows me to search through a database
> (yeast.nt*) *with a few queries (yeastquery.fasta). Here is the code:
> 
> *use warnings;*
> *use Bio::Tools::Run::Alignment::Blat;*
> *use Bio::SeqIO;*
> *use Bio::DB::Fasta;*
> *  *
> *my $seqio_object  = Bio::SeqIO -> new (-file =>
> 'C:/Users/MINH/Desktop/yeastquery.fasta',  -format => 'fasta'); *
> *        *
> *my $database = 'C:/Users/MINH/Desktop/yeast.nt';*
> *my $db = Bio::DB::Fasta->new($database); *
> *        *
> *my $factory = Bio::Tools::Run::Alignment::Blat->new(); *
> *
> *
> *while (my $blat_object = $seqio_object -> next_seq) {** *
> *                my $results = $factory -> run($blat_object,$db); *
> *}*
> 
> 
> BUT i got this error and don't know how to fix it. I am sorry, i am new to
> Perl and Bioperl. I am using window 7, Strawberry.
> 
> 
> *Replacement list is longer than search list at
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Chris Fields | 3 Jul 2010 20:27
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Re: Seeking comments, Bio::Species memleak fix

No comments.  I'm assuming this is okay to merge into master branch, so will merge in later today.

chris

On Jun 30, 2010, at 12:35 PM, Chris Fields wrote:

> All,
> 
> I have a branch in github (topic/species_proxy) that converts
> Bio::Species into a proxy class.  This appears to fix a ton of problems
> introduced during the Tree/Taxonomy refactoring a few years back.
> 
> Advantages:
> 
> 1) No need for Scalar::Util::weaken within Bio::Species or
> Bio::Tree::Node.  Cleanup methods are handled during instance
> destruction.
> 
> 2) This paves the way a bit more for eventual deprecation of
> Bio::Species in 1.7.
> 
> 3) Works with bioperl-db and BioSQL as is (passes on both my local
> Ubuntu 9.10 and Mac OS X 10.6), perl 5.10 and 5.12, should work with
> earlier perl versions.
> 
> Disadvantages:
> 
> 1) For every Bio::Species, we have a Bio::Taxon, a Bio::Tree::Tree, and
> a Bio::DB::Taxonomy (one instance more than the previous Bio::Species
> implementation).  We can probably reduce that down considerably by
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Hilmar Lapp | 3 Jul 2010 22:55
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Re: Seeking comments, Bio::Species memleak fix


On Jun 30, 2010, at 1:35 PM, Chris Fields wrote:

> Bio::Species had previously inherited from Bio::Taxon, but also  
> required
> it to hold a Bio::Tree::Tree which contained a circular reference back
> to the Bio::Species object, thus requiring Scalar::Util::weaken.  This
> has caused several hard-to-diagnose problems with premature garbage
> collection, including some issues with threads (bug 3017).

Is there something we should learn for future cases in which circular  
references are being considered with the S::U::weaken remedy (such as  
the recent one re: SeqI<->SeqFeatureI)?

	-hilmar
--

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================
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