rpms/perl-GO-TermFinder/devel GO-TermFinder-filter-provides.sh, NONE, 1.1 perl-GO-TermFinder.spec, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2

Jeroen van Meeuwen kanarip at fedoraproject.org
Thu May 22 19:47:51 UTC 2008

Author: kanarip

Update of /cvs/pkgs/rpms/perl-GO-TermFinder/devel
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv16286/devel

Modified Files:
	.cvsignore sources 
Added Files:
	GO-TermFinder-filter-provides.sh perl-GO-TermFinder.spec 
Log Message:

--- NEW FILE GO-TermFinder-filter-provides.sh ---

@@PERL_PROV@@ "$@" | sed -e '/^perl(Hang)$/d' \
    -e '/^perl(NullHang)$/d'

--- NEW FILE perl-GO-TermFinder.spec ---

Name:		perl-GO-TermFinder
Version:	0.82
Release:	2%{?dist}
Summary:	Identify GO nodes that annotate a group of genes with a significant p-value
License:	MIT
Group:		Development/Libraries
URL:		http://search.cpan.org/dist/Go-TermFinder/
Source0:	http://www.cpan.org/authors/id/S/SH/SHERLOCK/GO-TermFinder-%{version}.tar.gz
BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires:	perl(ExtUtils::MakeMaker), perl(Test::More)
BuildRequires:	perl(GD), perl(GraphViz)

Requires:	perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
Requires:	perl(Storable), perl(GD), perl(GraphViz), perl(CGI)

# Filter out perl(Hang) and perl(NullHang) auto-provides.
Source99:	GO-TermFinder-filter-provides.sh

%global real_perl_provides %{__perl_provides}
%define __perl_provides %{_tmppath}/%{name}-%{version}-%{release}-%(%{__id_u} -n)-filter-provides

This package is intended to provide a method whereby the P-values of a set
of GO annotations can be determined for a set of genes, based on the number
of genes that exist in the particular genome (or in a selected background
distribution from the genome), and their annotation, and the frequency with
which the GO nodes are annotated across the provided set of genes. The
P-value is simply calculated using the hypergeometric distribution as the
probability of x or more out of n genes having a given annotation, given
that G of N have that annotation in the genome in general. We chose the
hypergeometric distribution (sampling without replacement) since it is more
accurate, though slower to calculate, than the binomial distribution
(sampling with replacement).

%setup -q -n GO-TermFinder-%{version}
chmod a-x lib/GO/TermFinder.pm Changes README

sed -e 's,@@PERL_PROV@@,%{real_perl_provides},' %{SOURCE99} > %{__perl_provides}
chmod +x %{__perl_provides}

%{__perl} Makefile.PL INSTALLDIRS=vendor OPTIMIZE="$RPM_OPT_FLAGS"
make %{?_smp_mflags}



find $RPM_BUILD_ROOT -type f -name "*.bs" -exec rm -f {} \;
find $RPM_BUILD_ROOT -type f -name .packlist -exec rm -f {} \;
find $RPM_BUILD_ROOT -depth -type d -exec rmdir {} 2>/dev/null \;
find $RPM_BUILD_ROOT -type f -name "*.pm" -exec chmod 644 {} \;

%{_fixperms} $RPM_BUILD_ROOT/*

# this test seems to have issues with being unable to resolve the builder's
# hostname inside mock.
%{?!_with_termfinder_native: rm t/GO-TermFinder-Native.t }
make test

rm -rf $RPM_BUILD_ROOT %{__perl_provides}

%doc Changes README

* Wed May 21 2008 Jeroen van Meeuwen <kanarip at fedoraproject.org> - 0.82-2
- Add suggested BuildRequires as per review (#447559)

* Tue May 20 2008 Jeroen van Meeuwen <kanarip at fedoraproject.org> - 0.82-1
- Initial packaging

Index: .cvsignore
RCS file: /cvs/pkgs/rpms/perl-GO-TermFinder/devel/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- .cvsignore	22 May 2008 18:40:51 -0000	1.1
+++ .cvsignore	22 May 2008 19:47:03 -0000	1.2
@@ -0,0 +1 @@

Index: sources
RCS file: /cvs/pkgs/rpms/perl-GO-TermFinder/devel/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- sources	22 May 2008 18:40:51 -0000	1.1
+++ sources	22 May 2008 19:47:03 -0000	1.2
@@ -0,0 +1 @@
+ffebb282cdd3d8dbd5819d57d2c20d37  GO-TermFinder-0.82.tar.gz

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