[vcftools] Initial package import

[verdurin]

commit f1cf146943e3d3b05b61095c09a068ff9067a73a
Author: Adam Huffman <verdurin at fedoraproject.org>
Date:   Sun Jul 29 22:34:52 2012 +0100

    Initial package import

 .gitignore    |    1 +
 sources       |    1 +
 vcftools.spec |   95 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 97 insertions(+), 0 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index e69de29..990fecb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/vcftools_0.1.9.tar.gz
diff --git a/sources b/sources
index e69de29..6a6198a 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+57f3b8d7ecb26a12559595851607f023  vcftools_0.1.9.tar.gz
diff --git a/vcftools.spec b/vcftools.spec
new file mode 100644
index 0000000..14cef98
--- /dev/null
+++ b/vcftools.spec
@@ -0,0 +1,95 @@
+Name:		vcftools
+Version:	0.1.9
+Release:	1%{?dist}
+Summary:	VCF file manipulation tools
+
+Group:		Applications/Engineering
+License:	GPLv3 
+URL:		http://vcftools.sourceforge.net/
+Source0:	http://downloads.sourceforge.net/%{name}/%{name}_%{version}.tar.gz
+
+BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildRequires:	zlib-devel
+
+
+%description
+A program package designed for working with VCF files, such as those
+generated by the 1000 Genomes Project. The aim of VCFtools is to
+provide methods for working with VCF files: validating, merging,
+comparing and calculate some basic population genetic statistics.
+
+%prep
+%setup -q -n %{name}_%{version}
+#%patch0 -p1
+
+%build
+make %{?_smp_mflags} CPPFLAGS="%{optflags}"
+
+
+%install
+rm -rf %{buildroot}
+make install PREFIX=%{buildroot}/usr MODDIR="%{buildroot}/%{perl_vendorarch}" \
+BINDIR="%{buildroot}/%{_bindir}"
+
+install -m 0775 %{_builddir}/%{name}_%{version}/cpp/vcftools %{buildroot}/%{_bindir}
+
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc README.txt
+%{_bindir}/vcf-compare
+%{_bindir}/fill-aa
+%{_bindir}/fill-an-ac
+#%%{_bindir}/fill-rsIDs
+%{_bindir}/vcf-merge
+%{_bindir}/vcf-query
+%{_bindir}/vcf-annotate
+%{_bindir}/vcf-concat
+%{_bindir}/vcf-convert
+%{_bindir}/vcf-isec
+%{_bindir}/vcf-sort
+%{_bindir}/vcf-stats
+%{_bindir}/vcf-subset
+%{_bindir}/vcf-to-tab
+%{_bindir}/vcf-validator
+%attr(0755, root, root) %{_bindir}/vcftools
+%{perl_vendorarch}/FaSlice.pm
+%{perl_vendorarch}/Vcf.pm
+%{perl_vendorarch}/VcfStats.pm
+
+%changelog
+* Sun Jul 29 2012  <bloch at verdurin.com> - 0.1.9-1
+- Update to 0.1.9
+- Remove perl patch that's no longer needed
+
+* Thu Jan  5 2012 Adam Huffman <verdurin at fedoraproject.org> - 0.1.7-1
+- update to upstream release 0.1.7
+- remove fill-rsIDs
+- update Perl makefile patch
+
+* Sun Jul 31 2011 Adam Huffman <bloch at verdurin.com> - 0.1.6-1
+- update to 0.1.6
+
+* Tue May  3 2011 Adam Huffman <bloch at verdurin.com> - 0.1.5-2
+- minor fix to Jack's Perl patch
+- permissions fix
+- hardcoded path fix
+- cleaner Makefile fix
+
+* Sun May 1 2011 Jack Tanner <ihok at hotmail.com> - 0.1.5-1
+- bump to 0.1.5
+- rename compare-vcf, merge-vcf, and query-vcf to vcf-compare,
+  vcf-merge, and vcf-query
+- add VcfStats.pm to perl export
+- patch perl/Makefile to export VcfStats.pm
+
+* Mon Mar 21 2011 Adam Huffman <bloch at verdurin.com> - 0.1.4a-1
+- initial version
+- fix CPPFLAGS
+- fix hardcoded installation location
+