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commit a61f106149405adad752e49e49ce961355e5be81 Author: Andreas Tille <[email protected]> Date: Thu Dec 31 13:19:16 2015 +0100 New upstream version --- debian/changelog | 6 ++++++ 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 +++--- 6 files changed, 22 insertions(+), 16 deletions(-) diff --git a/debian/changelog b/debian/changelog index 531f9af..c207c37 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +sga (0.10.14-1) UNRELEASED; urgency=medium + + * New upstream version + + -- Andreas Tille <[email protected]> Thu, 31 Dec 2015 13:19:24 +0100 + sga (0.10.13-1) unstable; urgency=low * Initial release (Closes: #692332) diff --git a/debian/patches/0002-no-rpath.patch b/debian/patches/0002-no-rpath.patch index 3c64791..e5ca701 100644 --- a/debian/patches/0002-no-rpath.patch +++ b/debian/patches/0002-no-rpath.patch @@ -3,9 +3,9 @@ From: "Michael R. Crusoe" <[email protected]>, Date: Wed, 28 May 2014 07:40:21 +0200 Subject: no-rpath ---- sga.orig/src/configure.ac -+++ sga/src/configure.ac -@@ -32,7 +32,7 @@ +--- a/src/configure.ac ++++ b/src/configure.ac +@@ -32,7 +32,7 @@ AC_ARG_WITH(bamtools, AS_HELP_STRING([-- [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 @@ +@@ -52,7 +52,7 @@ AC_ARG_WITH(hoard, AS_HELP_STRING([--wit # 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 021353a..71d22ec 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(-) ---- sga-0.10.13.orig/src/bin/Makefile.am -+++ sga-0.10.13/src/bin/Makefile.am +--- a/src/bin/Makefile.am ++++ b/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 90bee90..b9cfa9f 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(-) ---- sga-0.10.13.orig/src/bin/sga-bam2de.pl -+++ sga-0.10.13/src/bin/sga-bam2de.pl -@@ -10,6 +10,7 @@ +--- a/src/bin/sga-bam2de.pl ++++ b/src/bin/sga-bam2de.pl +@@ -10,6 +10,7 @@ my $prefix = ""; 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 @@ +@@ -21,7 +22,13 @@ GetOptions("prefix=s" => \$prefix, "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 @@ +@@ -82,6 +89,7 @@ sub usage 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 58fad44..663488f 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(-) ---- sga-0.10.13.orig/src/bin/Makefile.am -+++ sga-0.10.13/src/bin/Makefile.am +--- a/src/bin/Makefile.am ++++ b/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 07bdf42..f970489 100644 --- a/debian/patches/0006-remove-google-addsense.patch +++ b/debian/patches/0006-remove-google-addsense.patch @@ -2,9 +2,9 @@ From: Andreas Tille <[email protected]> Date: Wed, 28 May 2014 07:40:21 +0200 Subject: remove Google analytics spying JavaScript ---- sga.orig/index.html -+++ sga/index.html -@@ -93,14 +93,5 @@ +--- a/index.html ++++ b/index.html +@@ -93,14 +93,5 @@ The package also contains programs to co </div> -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sga.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
