This is an automated email from the git hooks/post-receive script. chapmanb-guest pushed a commit to branch master in repository freebayes.
commit 0bfee0237c1ee96869c3443253b296b30bbd86ba Author: chapmanb <[email protected]> Date: Sun Feb 2 10:41:29 2014 -0500 Add patches for intial clean and cmake dependency --- .gitignore | 9 --------- debian/changelog | 2 +- debian/control | 15 ++++++++------- debian/patches/clean.patch | 8 +++----- debian/rules | 3 --- src/Makefile | 2 +- 6 files changed, 13 insertions(+), 26 deletions(-) diff --git a/.gitignore b/.gitignore index 7e817d2..e43b0f9 100644 --- a/.gitignore +++ b/.gitignore @@ -1,10 +1 @@ -test/ -bugs/ -*.bak -*~ -.Rhistory -simulation -src/libbamtools.a -performance -math .DS_Store diff --git a/debian/changelog b/debian/changelog index 9c70b47..7471511 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,5 @@ freebayes (0.9.10.11-1) UNRELEASED; urgency=low - * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + * Initial FreeBayes packaging (Closes: #nnnn) -- Brad Chapman <[email protected]> Sun, 02 Feb 2014 05:14:33 -0500 diff --git a/debian/control b/debian/control index f528923..734b026 100644 --- a/debian/control +++ b/debian/control @@ -2,7 +2,8 @@ Source: freebayes Section: science Priority: optional Maintainer: Brad Chapman <[email protected]> -Build-Depends: debhelper (>= 9) +Build-Depends: debhelper (>= 9), + cmake (>= 2) Standards-Version: 3.9.5 Homepage: https://github.com/ekg/freebayes Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/freebayes.git @@ -12,9 +13,9 @@ Package: freebayes Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Bayesian haplotype-based polymorphism discovery and genotyping - FreeBayes is a Bayesian genetic variant detector designed to find - small polymorphisms, specifically SNPs (single-nucleotide - polymorphisms), indels (insertions and deletions), MNPs - (multi-nucleotide polymorphisms), and complex events (composite - insertion and substitution events) smaller than the length of a - short-read sequencing alignment. \ No newline at end of file + FreeBayes is a Bayesian genetic variant detector designed to find + small polymorphisms, specifically SNPs (single-nucleotide + polymorphisms), indels (insertions and deletions), MNPs + (multi-nucleotide polymorphisms), and complex events (composite + insertion and substitution events) smaller than the length of a + short-read sequencing alignment. \ No newline at end of file diff --git a/debian/patches/clean.patch b/debian/patches/clean.patch index e5d43c1..34aefeb 100644 --- a/debian/patches/clean.patch +++ b/debian/patches/clean.patch @@ -1,12 +1,10 @@ -Index: freebayes/src/Makefile -=================================================================== ---- freebayes.orig/src/Makefile 2014-02-02 06:40:47.242351987 -0500 -+++ freebayes/src/Makefile 2014-02-02 06:42:43.390356892 -0500 +--- freebayes.orig/src/Makefile ++++ freebayes/src/Makefile @@ -259,6 +259,6 @@ clean: rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} - cd $(BAMTOOLS_ROOT)/build && make clean -+ test -d $(BAMTOOLS_ROOT)/build && cd $(BAMTOOLS_ROOT)/build && make clean ++ test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean) cd ../vcflib/smithwaterman && make clean diff --git a/debian/rules b/debian/rules index c30b66e..4067ba0 100755 --- a/debian/rules +++ b/debian/rules @@ -1,7 +1,4 @@ #!/usr/bin/make -f -# This has to be exported to make some magic below work. -export DH_OPTIONS - %: dh $@ diff --git a/src/Makefile b/src/Makefile index fc72a07..3fd822c 100644 --- a/src/Makefile +++ b/src/Makefile @@ -259,6 +259,6 @@ autoversion: clean: rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} - cd $(BAMTOOLS_ROOT)/build && make clean + test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean) cd ../vcflib/smithwaterman && make clean -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
