[BEDTools/f13/master] Initial import (#620385).

[verdurin]

commit 49314f86db9b087b985feeea46afa03d108bfe39
Author: Adam Huffman <bloch at verdurin.com>
Date:   Tue Sep 14 11:00:25 2010 +0100

    Initial import (#620385).

 .gitignore    |    2 +
 BEDTools.spec |  128 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 sources       |    2 +
 3 files changed, 132 insertions(+), 0 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index e69de29..592acff 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1,2 @@
+/BEDTools-User-Manual.v3.pdf
+/BEDTools.v2.9.0.tar.gz
diff --git a/BEDTools.spec b/BEDTools.spec
new file mode 100644
index 0000000..3d8f775
--- /dev/null
+++ b/BEDTools.spec
@@ -0,0 +1,128 @@
+Name:		BEDTools
+Version:	2.9.0
+Release:	5%{?dist}
+Summary:	A flexible suite of utilities for comparing genomic features
+
+Group:		Applications/Engineering
+License:	GPLv2+
+URL:		http://code.google.com/p/bedtools/
+
+# Download is listed in an RPM-unfriendly way on the Google Code site
+# The file can be obtained at
+# http://code.google.com/p/bedtools/downloads/detail?name=BEDTools.v2.9.0.tar.gz
+
+Source0:	http://bedtools.googlecode.com/files/%{name}.v%{version}.tar.gz
+Source1:	http://bedtools.googlecode.com/files/%{name}-User-Manual.v3.pdf
+BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildRequires:	  zlib-devel
+
+%description
+
+The BEDTools utilities allow one to address common genomics tasks such
+as finding feature overlaps and computing coverage. The utilities are
+largely based on four widely-used file formats: BED, GFF/GTF, VCF, and
+SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that
+answer complicated research questions by "streaming" several BEDTools
+together. 
+
+%package  docs
+Summary:  Manual for BEDTools
+Group:	  Documentation
+License:  GPLv2
+
+%description docs
+
+PDF manual for the BEDTools utilities.
+
+
+%prep
+%setup -q -n %{name}-Version-%{version}
+
+# remove bundled curl library
+rm -rf src/utils/curl
+
+# add manual
+cp -p %{SOURCE1} .
+
+%build
+# gzstream includes a local header file
+make %{?_smp_mflags} CXXFLAGS="-I. %{optflags}"
+
+
+%install
+rm -rf %{buildroot}
+
+mkdir -p %{buildroot}/%{_bindir}
+install -m 0755 bin/* %{buildroot}/%{_bindir}
+
+mkdir -p %{buildroot}/%{_datadir}/%{name}
+
+cp -a genomes/ %{buildroot}/%{_datadir}/%{name}
+cp -a data/ %{buildroot}/%{_datadir}/%{name}
+# fix permissions
+find %{buildroot}%{_datadir}/%{name} -type f -exec chmod 0644 {} \;
+
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc README RELEASE_HISTORY LICENSE 
+%dir %{_datadir}/%{name}
+%{_bindir}/bamToBed
+%{_bindir}/bed12ToBed6
+%{_bindir}/bedToBam
+%{_bindir}/bedToIgv
+%{_bindir}/closestBed
+%{_bindir}/complementBed
+%{_bindir}/coverageBed
+%{_bindir}/fastaFromBed
+%{_bindir}/genomeCoverageBed
+%{_bindir}/groupBy
+%{_bindir}/intersectBed
+%{_bindir}/linksBed
+%{_bindir}/maskFastaFromBed
+%{_bindir}/mergeBed
+%{_bindir}/overlap
+%{_bindir}/pairToBed
+%{_bindir}/pairToPair
+%{_bindir}/shuffleBed
+%{_bindir}/slopBed
+%{_bindir}/sortBed
+%{_bindir}/subtractBed
+%{_bindir}/unionBedGraphs
+%{_bindir}/windowBed
+
+%{_datadir}/%{name}/genomes
+%{_datadir}/%{name}/data
+
+%files docs
+%defattr(-,root,root,-)
+%doc %{name}-User-Manual.v3.pdf
+
+%changelog
+* Sun Sep 12 2010 Adam Huffman <bloch at verdurin.com> - 2.9.0-5
+- add license for -docs 
+
+* Wed Sep  1 2010 Adam Huffman <bloch at verdurin.com> - 2.9.0-4
+- add -docs subpackage including PDF manual
+
+* Tue Aug 31 2010 Adam Huffman <bloch at verdurin.com> - 2.9.0-3
+- remove 'curl' library properly
+
+* Tue Aug 31 2010 Adam Huffman <bloch at verdurin.com> - 2.9.0-2
+- fix license and add LICENSE file
+- fix permissions of data/
+- remove bundled 'curl' library
+
+* Wed Aug 25 2010 Adam Huffman <bloch at verdurin.com> - 2.9.0-1
+- new upstream release
+- add new unionBedGraphs tool
+
+* Mon Aug  2 2010 Adam Huffman <bloch at verdurin.com> - 2.8.3-1
+- initial version
+- override upstream CFLAGS
+- allow including gzstream header file
diff --git a/sources b/sources
index e69de29..cf75a79 100644
--- a/sources
+++ b/sources
@@ -0,0 +1,2 @@
+85e66413587f3f1cbb5e9530c20c6d1e  BEDTools-User-Manual.v3.pdf
+a0ac1e63fe4a7ae72e33fd91c24ac3da  BEDTools.v2.9.0.tar.gz