[mmseq] Update to 0.9.18

[verdurin]

commit 635a2bd552791ffb4567a2853c0dde854b940816
Author: Adam Huffman <verdurin at fedoraproject.org>
Date:   Wed Jan 11 15:09:21 2012 +0000

    Update to 0.9.18

 .gitignore       |    1 +
 mmseq-zlib.patch |   10 +++++-----
 mmseq.spec       |   17 +++++++++++------
 sources          |    2 +-
 4 files changed, 18 insertions(+), 12 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index 285d18a..6ff831c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 /mmseq_0.9.11.zip
 /mmseq_0.9.12.zip
 /mmseq_0.9.14.zip
+/mmseq_0.9.18.zip
diff --git a/mmseq-zlib.patch b/mmseq-zlib.patch
index 32eef80..27a3656 100644
--- a/mmseq-zlib.patch
+++ b/mmseq-zlib.patch
@@ -1,11 +1,11 @@
---- mmseq_0.9.10b/Makefile	2011-05-04 02:18:37.000000000 +0100
-+++ mmseq_0.9.10b.new/Makefile	2011-05-27 15:01:23.541812023 +0100
-@@ -6,7 +6,7 @@
+--- mmseq_0.9.18/Makefile	2011-12-16 14:44:46.000000000 +0000
++++ mmseq_0.9.18.new/Makefile	2012-01-11 15:03:03.091319510 +0000
+@@ -11,7 +11,7 @@
  CC = gcc
  CXX = g++
  LIBS = -lgsl -lgslcblas 
 -LIBS_B2H = -lboost_regex -lbam -lz
 +LIBS_B2H = -lboost_regex -lbam -Wl,--as-needed -lz
+ OMP = -fopenmp
+ OPT = -O3
  
- HPC_INCLUDE = -I /apps/boost/1.36.0/include -I /apps/gsl/1.8/include -L /apps/gsl/1.8/lib -I /home/et04/samtools
- HPC_LIB = -L /apps/boost/1.36.0/lib -L /apps/gsl/1.8/lib -L /home/et04/samtools
diff --git a/mmseq.spec b/mmseq.spec
index 7ea0ded..eb96c1e 100644
--- a/mmseq.spec
+++ b/mmseq.spec
@@ -1,6 +1,6 @@
 Name:		mmseq
-Version:	0.9.14
-Release:	2%{?dist}
+Version:	0.9.18
+Release:	1%{?dist}
 Summary:	Haplotype and isoform specific expression estimation for RNA-seq
 
 Group:		Applications/Engineering
@@ -8,7 +8,7 @@ License:	GPLv2+
 URL:		http://www.bgx.org.uk/software/mmseq.html
 Source0:	http://www.bgx.org.uk/software/%{name}_%{version}.zip
 Patch0:		mmseq-sam-header.patch
-Patch1:		mmseq-flags.patch
+#Patch1:		mmseq-flags.patch
 Patch2:		mmseq-zlib.patch
 BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
@@ -30,7 +30,7 @@ estimation using multi-mapping RNA-seq reads.  Example scripts are included.
 #Look for samtools headers in the correct location for Fedora
 %patch0 -p1 -b .mmseq-sam-header.patch
 #Use Fedora compilation headers
-%patch1 -p1 -b .mmseq-flags.patch
+#%%patch1 -p1 -b .mmseq-flags.patch
 #Fix zlib linking
 %patch2 -p1 -b .mmseq-zlib.patch
 
@@ -62,16 +62,21 @@ rm -rf %{buildroot}
 %{_bindir}/bam2hits
 %{_bindir}/mmseq
 %{_bindir}/fastagrep.sh
-%{_bindir}/pileup.sh
+#%%{_bindir}/pileup.sh
 %{_bindir}/routeB.sh
 %{_bindir}/filterGTF.rb
-%{_bindir}/get_isize.rb
+#%%{_bindir}/get_isize.rb
 %{_bindir}/haploref.rb
 %{_bindir}/testregexp.rb
 %{_bindir}/ensembl_gtf_to_gff.pl
 
 
 %changelog
+* Wed Jan 11 2012 Adam Huffman <verdurin at fedoraproject.org> - 0.9.18-1
+- update to 0.9.18
+- remove pileup.sh and get_isize.rb, discarded upstream
+- update patches and remove flags patch
+
 * Sun Nov 20 2011 Adam Huffman <adam at vaioz.verdurin.salon> - 0.9.14-2
 - rebuild for new Boost in Rawhide
 
diff --git a/sources b/sources
index 8c5efd6..89ba772 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-66356c90dc17a3c363d1742617667736  mmseq_0.9.14.zip
+96e2769b7083183fc80bd906286ae663  mmseq_0.9.18.zip