[med-svn] [sga] 03/04: Refresh patches
Afif Elghraoui
afif at moszumanska.debian.org
Mon Aug 22 07:44:58 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch debian/unstable
in repository sga.
commit 47f18d8232374eb63ca00b0547588b3520f569c7
Author: Afif Elghraoui <afif at debian.org>
Date: Mon Aug 22 00:18:24 2016 -0700
Refresh patches
---
debian/patches/0002-no-rpath.patch | 8 ++++----
debian/patches/0003-do-not-dist-unsup-script.patch | 4 ++--
debian/patches/0004-Add-help-to-sga-bam2de.pl.patch | 10 +++++-----
debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch | 4 ++--
debian/patches/0006-remove-google-addsense.patch | 6 +++---
5 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/debian/patches/0002-no-rpath.patch b/debian/patches/0002-no-rpath.patch
index e5ca701..3c64791 100644
--- a/debian/patches/0002-no-rpath.patch
+++ b/debian/patches/0002-no-rpath.patch
@@ -3,9 +3,9 @@ From: "Michael R. Crusoe" <michael.crusoe at gmail.com>,
Date: Wed, 28 May 2014 07:40:21 +0200
Subject: no-rpath
---- a/src/configure.ac
-+++ b/src/configure.ac
-@@ -32,7 +32,7 @@ AC_ARG_WITH(bamtools, AS_HELP_STRING([--
+--- 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
@@ -14,7 +14,7 @@ Subject: no-rpath
bamtools_include="-I$with_bamtools/include -I$with_bamtools/include/bamtools"
fi
-@@ -52,7 +52,7 @@ AC_ARG_WITH(hoard, AS_HELP_STRING([--wit
+@@ -52,7 +52,7 @@
# Set library path to user-selected allocator
if test "$with_hoard" -a -d "$with_hoard"; then
diff --git a/debian/patches/0003-do-not-dist-unsup-script.patch b/debian/patches/0003-do-not-dist-unsup-script.patch
index 71d22ec..31d84f5 100644
--- a/debian/patches/0003-do-not-dist-unsup-script.patch
+++ b/debian/patches/0003-do-not-dist-unsup-script.patch
@@ -6,8 +6,8 @@ Subject: do-not-dist-unsup-script
src/bin/Makefile.am | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
+--- sga.orig/src/bin/Makefile.am
++++ sga/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 b9cfa9f..2569234 100644
--- a/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
+++ b/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
@@ -6,9 +6,9 @@ Subject: Add --help to sga-bam2de.pl
src/bin/sga-bam2de.pl | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
---- a/src/bin/sga-bam2de.pl
-+++ b/src/bin/sga-bam2de.pl
-@@ -10,6 +10,7 @@ my $prefix = "";
+--- sga.orig/src/bin/sga-bam2de.pl
++++ sga/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
@@ -16,7 +16,7 @@ Subject: Add --help to sga-bam2de.pl
# 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,
@@ -31,7 +31,7 @@ Subject: Add --help to sga-bam2de.pl
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 663488f..e3c5a1e 100644
--- a/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
+++ b/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
@@ -6,8 +6,8 @@ Subject: Remove extensions on scripts we ship
src/bin/Makefile.am | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
+--- sga.orig/src/bin/Makefile.am
++++ sga/src/bin/Makefile.am
@@ -1,5 +1,10 @@
dist_bin_SCRIPTS = \
- sga-bam2de.pl \
diff --git a/debian/patches/0006-remove-google-addsense.patch b/debian/patches/0006-remove-google-addsense.patch
index f970489..07bdf42 100644
--- a/debian/patches/0006-remove-google-addsense.patch
+++ b/debian/patches/0006-remove-google-addsense.patch
@@ -2,9 +2,9 @@ From: Andreas Tille <tille at debian.org>
Date: Wed, 28 May 2014 07:40:21 +0200
Subject: remove Google analytics spying JavaScript
---- a/index.html
-+++ b/index.html
-@@ -93,14 +93,5 @@ The package also contains programs to co
+--- sga.orig/index.html
++++ sga/index.html
+@@ -93,14 +93,5 @@
</div>
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