verdurin pushed to samtools (epel7). "Merge branch 'master' into el5 (..more)"
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Sat May 30 07:33:14 UTC 2015
From ac1c9ae9d7417dfab5a566bfe71c91d3098133e2 Mon Sep 17 00:00:00 2001
From: Fedora Release Engineering <rel-eng at lists.fedoraproject.org>
Date: Thu, 29 Jul 2010 12:02:48 +0000
Subject: dist-git conversion
diff --git a/.cvsignore b/.cvsignore
deleted file mode 100644
index c62e948..0000000
--- a/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-samtools-0.1.7a.tar.bz2
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..c62e948
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+samtools-0.1.7a.tar.bz2
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 9b2eb19..0000000
--- a/Makefile
+++ /dev/null
@@ -1,21 +0,0 @@
-# Makefile for source rpm: samtools
-# $Id: Makefile,v 1.1 2009/07/12 16:58:23 tibbs Exp $
-NAME := samtools
-SPECFILE = $(firstword $(wildcard *.spec))
-
-define find-makefile-common
-for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$d/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
-endef
-
-MAKEFILE_COMMON := $(shell $(find-makefile-common))
-
-ifeq ($(MAKEFILE_COMMON),)
-# attept a checkout
-define checkout-makefile-common
-test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
-endef
-
-MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
-endif
-
-include $(MAKEFILE_COMMON)
diff --git a/import.log b/import.log
deleted file mode 100644
index 4a02c4e..0000000
--- a/import.log
+++ /dev/null
@@ -1,2 +0,0 @@
-samtools-0_1_5c-3_fc10:HEAD:samtools-0.1.5c-3.fc10.src.rpm:1247425812
-samtools-0_1_7a-1_fc11:HEAD:samtools-0.1.7a-1.fc11.src.rpm:1259569235
--
cgit v0.10.2
From 63a91910a97c9c35916b7e8c7a7fa9d5c03c90ad Mon Sep 17 00:00:00 2001
From: Rasmus Ory Nielsen <roni at woodstock.gbi.djf.agrsci.dk>
Date: Tue, 17 Aug 2010 10:34:01 +0200
Subject: Updated to 0.1.8
diff --git a/.gitignore b/.gitignore
index c62e948..7c27549 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
samtools-0.1.7a.tar.bz2
+/samtools-0.1.8.tar.bz2
diff --git a/samtools.spec b/samtools.spec
index f5d274f..4dacfbf 100644
--- a/samtools.spec
+++ b/samtools.spec
@@ -1,5 +1,5 @@
Name: samtools
-Version: 0.1.7a
+Version: 0.1.8
Release: 1%{?dist}
Summary: Tools for nucleotide sequence alignments in the SAM format
@@ -21,6 +21,9 @@ manipulating alignments in the SAM format.
%prep
%setup -q
+# fix wrong interpreter
+perl -pi -e "s[/software/bin/python][%{__python}]" misc/varfilter.py
+
%build
make CFLAGS="%{optflags}" samtools razip %{?_smp_mflags}
@@ -40,8 +43,9 @@ 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 sam2vcf.pl \
- samtools.pl soap2sam.pl wgsim wgsim_eval.pl zoom2sam.pl \
+ maq2sam-long maq2sam-short md5fa md5sum-lite novo2sam.pl psl2sam.pl \
+ sam2vcf.pl samtools.pl soap2sam.pl varfilter.py wgsim wgsim_eval.pl \
+ zoom2sam.pl \
%{buildroot}%{_bindir}
@@ -57,6 +61,9 @@ rm -rf %{buildroot}
%changelog
+* Tue Aug 17 2010 Rasmus Ory Nielsen <ron at ron.dk> - 0.1.8-1
+- Updated to 0.1.8.
+
* Mon Nov 30 2009 Rasmus Ory Nielsen <ron at ron.dk> - 0.1.7a-1
- Updated to 0.1.7a.
diff --git a/sources b/sources
index 40fd4ce..1ebcd9c 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-5e5aed8f0e0ec0009a3f0bb3e639c18b samtools-0.1.7a.tar.bz2
+db9e8d3acbe5dc040ff20a04a1bf1891 samtools-0.1.8.tar.bz2
--
cgit v0.10.2
From 947c8431d9ec779a09eb0c7aff226e66a5844bdb Mon Sep 17 00:00:00 2001
From: Rasmus Ory Nielsen <ron at fedoraproject.org>
Date: Tue, 17 Aug 2010 10:34:01 +0200
Subject: Updated to 0.1.8
diff --git a/.gitignore b/.gitignore
index c62e948..7c27549 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
samtools-0.1.7a.tar.bz2
+/samtools-0.1.8.tar.bz2
diff --git a/samtools.spec b/samtools.spec
index f5d274f..4dacfbf 100644
--- a/samtools.spec
+++ b/samtools.spec
@@ -1,5 +1,5 @@
Name: samtools
-Version: 0.1.7a
+Version: 0.1.8
Release: 1%{?dist}
Summary: Tools for nucleotide sequence alignments in the SAM format
@@ -21,6 +21,9 @@ manipulating alignments in the SAM format.
%prep
%setup -q
+# fix wrong interpreter
+perl -pi -e "s[/software/bin/python][%{__python}]" misc/varfilter.py
+
%build
make CFLAGS="%{optflags}" samtools razip %{?_smp_mflags}
@@ -40,8 +43,9 @@ 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 sam2vcf.pl \
- samtools.pl soap2sam.pl wgsim wgsim_eval.pl zoom2sam.pl \
+ maq2sam-long maq2sam-short md5fa md5sum-lite novo2sam.pl psl2sam.pl \
+ sam2vcf.pl samtools.pl soap2sam.pl varfilter.py wgsim wgsim_eval.pl \
+ zoom2sam.pl \
%{buildroot}%{_bindir}
@@ -57,6 +61,9 @@ rm -rf %{buildroot}
%changelog
+* Tue Aug 17 2010 Rasmus Ory Nielsen <ron at ron.dk> - 0.1.8-1
+- Updated to 0.1.8.
+
* Mon Nov 30 2009 Rasmus Ory Nielsen <ron at ron.dk> - 0.1.7a-1
- Updated to 0.1.7a.
diff --git a/sources b/sources
index 40fd4ce..1ebcd9c 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-5e5aed8f0e0ec0009a3f0bb3e639c18b samtools-0.1.7a.tar.bz2
+db9e8d3acbe5dc040ff20a04a1bf1891 samtools-0.1.8.tar.bz2
--
cgit v0.10.2
From 158cb20973cf650dc1d4c1bcbba5eacd9abbfedb Mon Sep 17 00:00:00 2001
From: Rasmus Ory Nielsen <ron at fedoraproject.org>
Date: Tue, 17 Aug 2010 11:23:26 +0200
Subject: Removed old source file name
diff --git a/.gitignore b/.gitignore
index 7c27549..846cb0e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1 @@
-samtools-0.1.7a.tar.bz2
/samtools-0.1.8.tar.bz2
--
cgit v0.10.2
http://pkgs.fedoraproject.org/cgit/samtools.git/commit/?h=epel7&id=7b6a5ce1474633c1d9774a8e69b12cb746dbcf17
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