From 2d917921026af734967890b570609aeb1f320afe Mon Sep 17 00:00:00 2001
From: ron <ron@fedoraproject.org>
Date: Jul 12 2009 19:10:51 +0000
Subject: Auto import of samtools.


---

diff --git a/.cvsignore b/.cvsignore
index e69de29..3c27903 100644
--- a/.cvsignore
+++ b/.cvsignore
@@ -0,0 +1 @@
+samtools-0.1.5c.tar.bz2
diff --git a/import.log b/import.log
new file mode 100644
index 0000000..29d62f3
--- /dev/null
+++ b/import.log
@@ -0,0 +1 @@
+samtools-0_1_5c-3_fc10:HEAD:samtools-0.1.5c-3.fc10.src.rpm:1247425812
diff --git a/samtools-0.1.5c-compilefix.patch b/samtools-0.1.5c-compilefix.patch
new file mode 100644
index 0000000..aa76f69
--- /dev/null
+++ b/samtools-0.1.5c-compilefix.patch
@@ -0,0 +1,11 @@
+diff -up samtools-0.1.5c/misc/Makefile.compilefix samtools-0.1.5c/misc/Makefile
+--- samtools-0.1.5c/misc/Makefile.compilefix	2009-07-11 15:33:04.000000000 +0200
++++ samtools-0.1.5c/misc/Makefile	2009-07-11 15:33:22.000000000 +0200
+@@ -1,6 +1,6 @@
+ CC=			gcc
+ CXX=		g++
+-CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
++CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
+ CXXFLAGS=	$(CFLAGS)
+ DFLAGS=		-D_FILE_OFFSET_BITS=64
+ OBJS=		
diff --git a/samtools.spec b/samtools.spec
new file mode 100644
index 0000000..089f2ff
--- /dev/null
+++ b/samtools.spec
@@ -0,0 +1,69 @@
+Name:		samtools
+Version:	0.1.5c
+Release:	3%{?dist}
+Summary:	Tools for nucleotide sequence alignments in the SAM format
+
+Group:		Applications/Engineering
+License:	MIT
+URL:		http://samtools.sourceforge.net/
+Source0:	http://downloads.sourceforge.net/%{name}/%{name}-%{version}.tar.bz2
+Patch0:		samtools-0.1.5c-compilefix.patch
+BuildRoot:	%(mktemp -ud %{_tmppath}/%{name}-%{version}-%{release}-XXXXXX)
+
+BuildRequires:	zlib-devel >= 1.2.3
+BuildRequires:	ncurses-devel
+
+%description
+SAM (Sequence Alignment/Map) is a flexible generic format for storing
+nucleotide sequence alignment. SAM tools provide efficient utilities on
+manipulating alignments in the SAM format.
+
+
+%prep
+%setup -q
+%patch0 -p1 -b .compilefix
+
+
+%build
+make CFLAGS="%{optflags}" samtools razip %{?_smp_mflags}
+
+cd misc/
+make CFLAGS="%{optflags}" %{?_smp_mflags}
+
+
+%install
+rm -rf %{buildroot}
+mkdir -p %{buildroot}%{_bindir}
+install -p samtools razip %{buildroot}%{_bindir}
+
+gzip samtools.1
+mkdir -p %{buildroot}%{_mandir}/man1/
+cp -p samtools.1.gz %{buildroot}%{_mandir}/man1/
+
+cd misc/
+install -p blast2sam.pl bowtie2sam.pl export2sam.pl interpolate_sam.pl \
+  maq2sam-long maq2sam-short md5fa md5sum-lite novo2sam.pl samtools.pl \
+  soap2sam.pl wgsim wgsim_eval.pl zoom2sam.pl %{buildroot}%{_bindir}
+
+
+%clean
+rm -rf %{buildroot}
+
+
+%files
+%defattr(-,root,root,-)
+%doc AUTHORS ChangeLog COPYING INSTALL NEWS source.dot examples/
+%{_bindir}/*
+%{_mandir}/man1/*
+
+
+%changelog
+* Sun Jul 12 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.5c-3
+- Specfile cleanup.
+
+* Sat Jul 11 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.5c-2
+- Fixed manpage location.
+- Make sure optflags is passed to the makefiles.
+
+* Sat Jul 11 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.5c-1
+- Initial build.
diff --git a/sources b/sources
index e69de29..d58f549 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+62551fbad3f7c63c52fad99c3baf8580  samtools-0.1.5c.tar.bz2