This is an automated email from the git hooks/post-receive script. chapmanb-guest pushed a commit to branch master in repository freebayes.
commit 70a2413b64920ab37a5f6c7fea90aa6374a7cc0c Author: chapmanb <[email protected]> Date: Sun Feb 2 06:48:54 2014 -0500 Add debian build files and patches --- .gitignore | 1 - debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 20 ++++++++++++++++++++ debian/copyright | 35 +++++++++++++++++++++++++++++++++++ debian/install | 2 ++ debian/patches/clean.patch | 12 ++++++++++++ debian/patches/series | 1 + debian/rules | 7 +++++++ debian/source/format | 1 + debian/upstream | 8 ++++++++ debian/watch | 7 +++++++ 12 files changed, 99 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index a68208e..7e817d2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,6 @@ test/ bugs/ *.bak -*.patch *~ .Rhistory simulation diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..9c70b47 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +freebayes (0.9.10.11-1) UNRELEASED; urgency=low + + * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + + -- Brad Chapman <[email protected]> Sun, 02 Feb 2014 05:14:33 -0500 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..f11c82a --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 \ No newline at end of file diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..f528923 --- /dev/null +++ b/debian/control @@ -0,0 +1,20 @@ +Source: freebayes +Section: science +Priority: optional +Maintainer: Brad Chapman <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.5 +Homepage: https://github.com/ekg/freebayes +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/freebayes.git +Vcs-Git: git://anonscm.debian.org/debian-med/freebayes.git + +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 diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..0b32fa0 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,35 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: freebayes +Source: https://github.com/ekg/freebayes + +Files: * +Copyright: 2010-2014 Erik Garrison, Gabor Marth +License: MIT + +Files: debian/* +Copyright: 2014 Brad Chapman <[email protected]> +License: MIT + +License: MIT + Permission is hereby granted, free of charge, to any person obtaining a + copy of this software and associated documentation files (the "Software"), + to deal in the Software without restriction, including without limitation + the rights to use, copy, modify, merge, publish, distribute, sublicense, + and/or sell copies of the Software, and to permit persons to whom the + Software is furnished to do so, subject to the following conditions: + . + The above copyright notice and this permission notice shall be included + in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS + OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. + IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY + CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, + TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE + SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +# Please also look if there are files or directories which have a +# different copyright/license attached and list them here. +# Please avoid to pick license terms that are more restrictive than the +# packaged work, as it may make Debian's contributions unacceptable upstream. diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..f82faed --- /dev/null +++ b/debian/install @@ -0,0 +1,2 @@ +bin/freebayes usr/bin +bin/bamleftalign usr/bin \ No newline at end of file diff --git a/debian/patches/clean.patch b/debian/patches/clean.patch new file mode 100644 index 0000000..e5d43c1 --- /dev/null +++ b/debian/patches/clean.patch @@ -0,0 +1,12 @@ +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 +@@ -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 + cd ../vcflib/smithwaterman && make clean + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..5df678c --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +clean.patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..c30b66e --- /dev/null +++ b/debian/rules @@ -0,0 +1,7 @@ +#!/usr/bin/make -f + +# This has to be exported to make some magic below work. +export DH_OPTIONS + +%: + dh $@ diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream b/debian/upstream new file mode 100644 index 0000000..eb3d836 --- /dev/null +++ b/debian/upstream @@ -0,0 +1,8 @@ +Reference: + Author: Erik Garrison and Gabor Marth + Title: Haplotype-based variant detection from short-read sequencing + Journal: arXiv + Year: 2012 + DOI: arXiv:1207.3907 + URL: http://arxiv.org/abs/1207.3907 + eprint: http://arxiv.org/pdf/1207.3907v2.pdf diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..34b97ca --- /dev/null +++ b/debian/watch @@ -0,0 +1,7 @@ +version=3 + +# Need to manually clone and tar/gzip from GitHub +# git clone --recursive git://github.com/ekg/freebayes.git +# For eventual releases: +opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/<project>-$1\.tar\.gz/ \ + https://github.com/<user>/<project>/tags .*/v?(\d\S*)\.tar\.gz \ No newline at end of file -- 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
