[Bioperl-l] RPMs for bioperl (... and GBrowse, and lsid-perl, and biomoby)

[Allen Day]

On Wed, 26 Jan 2005, Lincoln Stein wrote:

> I'm glad you're doing this.
> 
> Can you simply turn off the warning messages about 
> Ace::Browser::LocalSiteDefs, Bio::Das::ProServer::SourceHydra, and 
> MOBY::*?  They are all optional and won't do anything useful without 
> a lot of extra configuration.

I could do that by creating the specfiles by hand, but I'd rather not do
this.  Is it difficult to just add the Bio::* and Ace::* modules to their
respective CPAN modules?

==========
% grep -r 'Hydra' ./Bio-Das-0.99/*
./Bio-Das-0.99/Das/ProServer/Config.pm:use Bio::Das::ProServer::SourceHydra;
./Bio-Das-0.99/Das/ProServer/Config.pm:# build all known SourceAdaptors (including those Hydra-based)
./Bio-Das-0.99/Das/ProServer/Config.pm:# build SourceHydra for a given dsn/hydraname
./Bio-Das-0.99/Das/ProServer/Config.pm:    my $hydraimpl = "Bio::Das::ProServer::SourceHydra::".$self->{'adaptors'}->{$hydraname}->{'hydra'};
==========

Missing SourceHydra.pm

==========
% grep -r 'Ace::Browser::LocalSiteDefs' ./AcePerl-1.87/*
./AcePerl-1.87/Ace/Browser/SiteDefs.pm:use Ace::Browser::LocalSiteDefs '$SITE_DEFS';
./AcePerl-1.87/acebrowser/conf/moviedb.pm:use Ace::Browser::LocalSiteDefs '$HTML_PATH';
./AcePerl-1.87/acebrowser/conf/default.pm:use Ace::Browser::LocalSiteDefs '$HTML_PATH';
./AcePerl-1.87/acebrowser/conf/simple.pm:use Ace::Browser::LocalSiteDefs '$HTML_PATH';
./AcePerl-1.87/Makefile.PL:  eval 'use Ace::Browser::LocalSiteDefs qw($SITE_DEFS $CGI_PATH $HTML_PATH)';
./AcePerl-1.87/Makefile.PL:package Ace::Browser::LocalSiteDefs;
./AcePerl-1.87/Makefile.PL:Ace::Browser::LocalSiteDefs - Master Configuration file for AceBrowser
./AcePerl-1.87/Makefile.PL: use Ace::Browser::LocalSiteDefs qw($SITE_DEFS $HTML_PATH $CGI_PATH);
./AcePerl-1.87/README.ACEBROWSER:Ace::Browser::LocalSiteDefs, typically somewhere inside the
./AcePerl-1.87/README.ACEBROWSER:  perl -MAce::Browser::LocalSiteDefs \
./AcePerl-1.87/README.ACEBROWSER:       -e 'print $Ace::Browser::LocalSiteDefs::SITE_DEFS,"\n"'
==========

LocalSiteDefs.pm does't exist, because package Ace::Browser::LocalSiteDefs
is, interestingly, defined in Makefile.PL and not installed.  Can we make
this a separate file, or at least define it in a file that is installed?

MOBY::*

If I fetch the biomoby and lsid-perl tarballs here: 
http://biomoby.org/releases/, and here: 
http://www-124.ibm.com/developerworks/oss/lsid/reference/tutorials/100/

I can resolve most of the MOBY::* requirements with this file.  These are
what's left:

  perl(MOBY::lsid::authority::dbConfigure) is needed by perl-biomoby-0.8.1-allenday
  perl(MOBY::MobyXMLConstants) is needed by perl-Generic-Genome-Browser-1.62-allenday

Is it possible to get releases onto CPAN of both biomoby and lsid-perl,
and to add these two MOBY files to MOBY?

Win32::Registry

This was introduced by lsid-perl by way of a Net::DNS requirement.  I'm
not sure what to do here.  Looks like I may need to handcode a specfile
here...

PPM::Archive

Where can I get this?  Looks like I may need to handcode a specfile
here...


> GuessDirectories.pm is a GBrowse install utility that is part of the 
> package.  I don't know why the RPM tool is complaining about it.

i think it has to do with the way the rpm build process identifies what
modules are "use"d.  from what i surmise, two lists are included in the
RPM, (1) a list of modules the package depends on, and (2) a list of
modules the package provides.  So in the case of Gbrowse's dependency on 
GuessDirectories, my guess is that it isn't correctly detecting 
GuessDirectories is provided by the package.  A quick look in the 
Generic-Genome-Browser checkout shows the module is referenced in a few 
places, but not actually included in the distribution:

==========
% grep -r 'GuessDirectories' Generic-Genome-Browser/*
Generic-Genome-Browser/install_util/CVS/Entries:/GuessDirectories.pm/1.1/Sun Jun  8 23:29:48 2003//Generic-Genome-Browser/Makefile.PL:use GuessDirectories;
Generic-Genome-Browser/Makefile.PL:  $OPTIONS{CONF} = GuessDirectories->conf || "$OPTIONS{APACHE}/conf";
Generic-Genome-Browser/Makefile.PL:  $OPTIONS{HTDOCS} = GuessDirectories->htdocs || "$OPTIONS{APACHE}/htdocs";
Generic-Genome-Browser/Makefile.PL:  $OPTIONS{CGIBIN} = GuessDirectories->cgibin || "$OPTIONS{APACHE}/cgi-bin";
Generic-Genome-Browser/MANIFEST:install_util/GuessDirectories.pm
==========

notice that there isn't a file containing 'package GuessDirectories;'.  
can you please add install_util/GuessDirectories.pm to the repository?

> I don't know about  IndexSupport.  What is it?

A download of Bio::Das 0.99 from: http://search.cpan.org/~lds/Bio-Das-0.99/
reveals:

% grep -r IndexSupport Bio-Das-0.99
Bio-Das-0.99/Das/ProServer/SourceAdaptor/haplotype.pm:use IndexSupport;
Bio-Das-0.99/Das/ProServer/SourceAdaptor/haplotype.pm:     my $conf = IndexSupport->new("$root/conf",'','Homo_sapiens');
Bio-Das-0.99/Das/ProServer/SourceAdaptor/snp.pm:use IndexSupport;Bio-Das-0.99/Das/ProServer/SourceAdaptor/snp.pm:     my $conf = IndexSupport->new("$root/conf",'','Homo_sapiens');
Bio-Das-0.99/Das/ProServer/SourceAdaptor/sts.pm:use IndexSupport;
Bio-Das-0.99/Das/ProServer/SourceAdaptor/sts.pm:     my $conf = IndexSupport->new("$root/conf",'','Homo_sapiens');
Bio-Das-0.99/Das/ProServer/SourceAdaptor/trace.pm:use IndexSupport;
Bio-Das-0.99/Das/ProServer/SourceAdaptor/trace.pm:     my $conf = IndexSupport->new("$root/conf",'','Homo_sapiens');

notice that there isn't a file containing 'package IndexSupport;'.  can
you please add IndexSupport.pm to the CPAN released module?  
interestingly, there is no reference to IndexSupport in the open-bio das 
repository.

-allen

> 
> Lincoln
> 
> On Wednesday 26 January 2005 01:27 am, Allen Day wrote:
> > Hi,
> >
> > I've put together a set of RPMs for Bioperl, Bioperl-DB,
> > Bioperl-Run, and GBrowse.  It's still a work in progress, but you
> > can see the current state here:
> >   http://sumo.genetics.ucla.edu/~allenday/flute/bioperl-1.5/i686/
> > There are some related directories rooted here:
> >   http://sumo.genetics.ucla.edu/~allenday/flute/
> >
> > The RPMs don't install clean.  This is because I'm using an
> > automated tool to build the RPMs, and it looks through each
> > downloaded tarball from CPAN to see what that tarball depends on. 
> > Sometimes there are dependencies on libraries that don't exist on
> > CPAN, or might be altogether non-existent. These are the problem
> > libraries and binaries:
> >
> > % rpm -Uvh --test *.rpm
> > error: Failed dependencies:
> >         perl(Ace::Browser::LocalSiteDefs) is needed by
> > perl-AcePerl-1.87-allenday perl(Bio::Das::ProServer::SourceHydra)
> > is needed by perl-Bio-Das-0.99-allenday perl(IndexSupport) is
> > needed by perl-Bio-Das-0.99-allenday perl(srsperl) is needed by
> > perl-bioperl-1.5.0-allenday perl(Bio::DB::BioDB) is needed by
> > perl-Generic-Genome-Browser-1.62-allenday
> > perl(Bio::DB::Query::BioQuery) is needed by
> > perl-Generic-Genome-Browser-1.62-allenday perl(GuessDirectories) is
> > needed by perl-Generic-Genome-Browser-1.62-allenday
> > perl(MOBY::Client::Central) is needed by
> > perl-Generic-Genome-Browser-1.62-allenday
> > perl(MOBY::Client::Service) is needed by
> > perl-Generic-Genome-Browser-1.62-allenday perl(MOBY::CommonSubs) is
> > needed by perl-Generic-Genome-Browser-1.62-allenday
> > perl(MOBY::MobyXMLConstants) is needed by
> > perl-Generic-Genome-Browser-1.62-allenday perl(PPM::Archive) is
> > needed by perl-Generic-Genome-Browser-1.62-allenday
> > perl(MQClient::MQSeries) is needed by perl-SOAP-Lite-0.60-allenday
> > perl(MQSeries) is needed by perl-SOAP-Lite-0.60-allenday
> > perl(MQSeries::Message) is needed by perl-SOAP-Lite-0.60-allenday
> > perl(MQSeries::Queue) is needed by perl-SOAP-Lite-0.60-allenday
> > perl(MQSeries::QueueManager) is needed by
> > perl-SOAP-Lite-0.60-allenday /bin/perl is needed by
> > perl-Tk-804.027-allenday
> >         /usr/local/bin/perl is needed by perl-Tk-804.027-allenday
> >         perl(Tk::LabRadio) is needed by perl-Tk-804.027-allenday
> >         perl(Tk::TextReindex) is needed by perl-Tk-804.027-allenday
> >         perl(XML::LibXML) >= 1.57 is needed by
> > perl-XML-LibXSLT-1.57-allenday perl(XML::SAX::PurePerl::DTDDecls)
> > is needed by perl-XML-SAX-0.12-allenday
> > perl(XML::SAX::PurePerl::DocType) is needed by
> > perl-XML-SAX-0.12-allenday perl(XML::SAX::PurePerl::EncodingDetect)
> > is needed by perl-XML-SAX-0.12-allenday
> > perl(XML::SAX::PurePerl::XMLDecl) is needed by
> > perl-XML-SAX-0.12-allenday
> >
> > Lincoln, I'm guessing you can help me with:
> >
> > * Ace::Browser::LocalSiteDefs
> > * Bio::Das::ProServer::SourceHydra
> > * GuessDirectories
> > * IndexSupport
> > * MOBY::*
> >
> > Hilmar, do you know about:
> >
> > * Bio::DB::BioDB
> > * Bio::DB::Query::BioQuery
> >
> > I'm sure someone on this list knows where to get
> >
> > * srsperl
> > * PPM::Archive
> >
> > If anyone can shed light on where any of these libraries can be
> > found, I'd appreciate it.  Thanks.
> >
> > -Allen
> >
> >
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