[med-svn] [freebayes] 02/03: Add debian build files and patches
Brad Chapman
chapmanb-guest at moszumanska.debian.org
Sun Feb 2 15:53:40 UTC 2014
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 <chapmanb at 50mail.com>
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 <chapmanb at 50mail.com> 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 <chapmanb at 50mail.com>
+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 <chapmanb at 50mail.com>
+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
More information about the debian-med-commit
mailing list