[med-svn] [sga] 06/10: Update patches to new upstream version
Andreas Tille
tille at debian.org
Wed May 28 12:48:42 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian
in repository sga.
commit a532e5eca008be278f57b3984fed6ce22ee0b2a7
Author: Andreas Tille <tille at debian.org>
Date: Wed May 28 09:17:53 2014 +0200
Update patches to new upstream version
---
debian/patches/0002-no-rpath.patch | 27 +++++++++-------------
debian/patches/0003-do-not-dist-unsup-script.patch | 6 ++---
.../patches/0004-Add-help-to-sga-bam2de.pl.patch | 12 ++++------
...0005-Remove-extensions-on-scripts-we-ship.patch | 6 ++---
debian/patches/series | 2 +-
5 files changed, 21 insertions(+), 32 deletions(-)
diff --git a/debian/patches/0002-no-rpath.patch b/debian/patches/0002-no-rpath.patch
index 175dfd7..3c64791 100644
--- a/debian/patches/0002-no-rpath.patch
+++ b/debian/patches/0002-no-rpath.patch
@@ -1,16 +1,11 @@
-From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
-Date: Wed, 7 Nov 2012 22:55:19 -0700
+From: "Michael R. Crusoe" <michael.crusoe at gmail.com>,
+ Andreas Tille <tille at debian.org>
+Date: Wed, 28 May 2014 07:40:21 +0200
Subject: no-rpath
----
- src/configure.ac | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/configure.ac b/src/configure.ac
-index b077d3d..86026e8 100644
---- a/src/configure.ac
-+++ b/src/configure.ac
-@@ -34,7 +34,7 @@ AC_ARG_WITH(bamtools, AS_HELP_STRING([--with-bamtools=PATH],
+--- sga.orig/src/configure.ac
++++ sga/src/configure.ac
+@@ -32,7 +32,7 @@
[specify directory containing the bamtools library (http://github.com/pezmaster31/bamtools)]))
if test "$with_bamtools" -a -d "$with_bamtools"; then
@@ -19,12 +14,12 @@ index b077d3d..86026e8 100644
bamtools_include="-I$with_bamtools/include -I$with_bamtools/include/bamtools"
fi
-@@ -42,7 +42,7 @@ fi
- AC_ARG_WITH(hoard, AS_HELP_STRING([--with-hoard=PATH],
- [specify directory containing the hoard memory allocator library]))
+@@ -52,7 +52,7 @@
+
+ # Set library path to user-selected allocator
if test "$with_hoard" -a -d "$with_hoard"; then
-- hoard_ldflags="-Wl,-rpath,$with_hoard -L$with_hoard"
-+ hoard_ldflags="-L$with_hoard"
+- external_malloc_ldflags="-Wl,-rpath,$with_hoard -L$with_hoard"
++ external_malloc_ldflags="-L$with_hoard"
enable_hoard=1
fi
diff --git a/debian/patches/0003-do-not-dist-unsup-script.patch b/debian/patches/0003-do-not-dist-unsup-script.patch
index 1a7a929..021353a 100644
--- a/debian/patches/0003-do-not-dist-unsup-script.patch
+++ b/debian/patches/0003-do-not-dist-unsup-script.patch
@@ -6,10 +6,8 @@ Subject: do-not-dist-unsup-script
src/bin/Makefile.am | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
-diff --git a/src/bin/Makefile.am b/src/bin/Makefile.am
-index 6ecd983..d250fda 100644
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
+--- sga-0.10.13.orig/src/bin/Makefile.am
++++ sga-0.10.13/src/bin/Makefile.am
@@ -1,6 +1,5 @@
dist_bin_SCRIPTS = \
- sga-astat.py \
diff --git a/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch b/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
index cbcf5a6..90bee90 100644
--- a/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
+++ b/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
@@ -6,11 +6,9 @@ Subject: Add --help to sga-bam2de.pl
src/bin/sga-bam2de.pl | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
-diff --git a/src/bin/sga-bam2de.pl b/src/bin/sga-bam2de.pl
-index 68c7649..f92825e 100755
---- a/src/bin/sga-bam2de.pl
-+++ b/src/bin/sga-bam2de.pl
-@@ -10,6 +10,7 @@ my $prefix = "";
+--- sga-0.10.13.orig/src/bin/sga-bam2de.pl
++++ sga-0.10.13/src/bin/sga-bam2de.pl
+@@ -10,6 +10,7 @@
my $numThreads = 1;
my $mind = -99; # minimum gap size to pass to abyss
my $mina = 100; # minimum alignment length to pass to abyss
@@ -18,7 +16,7 @@ index 68c7649..f92825e 100755
# Filter the abyss distance est histogram to remove insert sizes
# with fewer than hist_min data points
-@@ -21,7 +22,13 @@ GetOptions("prefix=s" => \$prefix,
+@@ -21,7 +22,13 @@
"m=i" => \$minLength,
"mind=i" => \$mind,
"mina=i" => \$mina,
@@ -33,7 +31,7 @@ index 68c7649..f92825e 100755
checkDependency("abyss-fixmate");
checkDependency("DistanceEst");
-@@ -82,6 +89,7 @@ sub usage
+@@ -82,6 +89,7 @@
print " --mind D Set the minimum distance estimate to test to be D. This should be a negative\n";
print " number if contigs are expected to overlap. Defaults to -99bp.\n";
print " --mina N Set the minimum alignment length to be N.\n";
diff --git a/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch b/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
index bcd8402..58fad44 100644
--- a/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
+++ b/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
@@ -6,10 +6,8 @@ Subject: Remove extensions on scripts we ship
src/bin/Makefile.am | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
-diff --git a/src/bin/Makefile.am b/src/bin/Makefile.am
-index d250fda..fe99513 100644
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
+--- sga-0.10.13.orig/src/bin/Makefile.am
++++ sga-0.10.13/src/bin/Makefile.am
@@ -1,5 +1,10 @@
dist_bin_SCRIPTS = \
- sga-bam2de.pl \
diff --git a/debian/patches/series b/debian/patches/series
index 0aa081a..80d6e4b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
-0001-no-Werror.patch
+# 0001-no-Werror.patch
0002-no-rpath.patch
0003-do-not-dist-unsup-script.patch
0004-Add-help-to-sga-bam2de.pl.patch
--
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