[med-svn] [unanimity] 03/10: Initial packaging
Afif Elghraoui
afif at moszumanska.debian.org
Fri Dec 23 10:34:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository unanimity.
commit dfc19f9e371c999a6d6b9a3051582868f6b052b2
Author: Afif Elghraoui <afif at debian.org>
Date: Tue Dec 6 23:08:48 2016 -0800
Initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 41 +++++++++++++++++++++++++++++++++++++
debian/copyright | 13 ++++++++++++
debian/get-orig-source | 55 ++++++++++++++++++++++++++++++++++++++++++++++++++
debian/rules | 30 +++++++++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 39 +++++++++++++++++++++++++++++++++++
8 files changed, 185 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..aacfcc3
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+unanimity (2.0.2+20160812+ds-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Afif Elghraoui <afif at debian.org> Fri, 12 Aug 2016 22:35:41 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9c01f9b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,41 @@
+Source: unanimity
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>
+Build-Depends:
+ debhelper (>= 9),
+ dh-python,
+ cmake,
+ swig,
+ python-all-dev,
+ python-numpy,
+ libboost-dev,
+ libhts-dev,
+ libpbbam-dev,
+ libpbcopper-dev,
+ libseqan2-dev,
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/packages/unanimity
+Vcs-Git: https://anonscm.debian.org/git/debian-med/packages/unanimity
+Homepage: https://github.com/PacificBiosciences/unanimity
+
+Package: unanimity
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends},
+ libpbbam,
+Description: Pacific Biosciences nucleotide sequencing consensus
+ <long_description>
+
+#Package: python-consensuscore2
+#Section: python
+#Architecture: any
+#Depends:
+# ${shlibs:Depends},
+# ${misc:Depends},
+# ${python:Depends},
+#Description: consensuscore2
+# long description of consensuscore2
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..2cb6c8f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,13 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: https://github.com/PacificBiosciences/unanimity
+Files-Excluded:
+ third-party/cram-*
+
+Files: *
+Copyright: 2016 Pacific Biosciences of California
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..2aa782f
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,55 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+# Excluding files and repacking archives
+# --------------------------------------
+# See also mk-origtargz(1) and the --repack option to uscan(1), which
+# honor the Files-Excluded list in debian/copyright.
+# That may be all you need, especially since the repack option can be set
+# in debian/watch.
+
+# For an example how to fetch source from sourceforge SVN see
+# https://anonscm.debian.org/git/debian-med/kmer-tools.git
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --force-download
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+tar -xaf ../${TARDIR}.tar.gz
+
+UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d`
+if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then
+ mv "${UPSTREAMTARDIR}" "${TARDIR}"
+fi
+
+# Remove useless binaries
+# ... do something which needs to be done ...
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e918bc5
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,30 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+include /usr/share/dpkg/architecture.mk
+export LC_ALL=C.UTF-8
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+export INCLUDE=/usr/include
+export LIB=/usr/lib/$(DEB_HOST_MULTIARCH)
+
+%:
+ dh $@ --with python2 --buildsystem=cmake
+
+override_dh_auto_configure:
+ dh_auto_configure -- \
+ -DUNY_build_tests=OFF \
+ -DPYTHON_SWIG=ON \
+# -DZLIB_INCLUDE_DIRS= \
+# -DZLIB_LIBRARIES= \
+# -DBoost_INCLUDE_DIRS= \
+# -DPacBioBAM_INCLUDE_DIRS= \
+# -DPacBioBAM_LIBRARIES=$(LIB)/libpbbam.so \
+# -DSEQAN_INCLUDE_DIRS=
+# -Dpbcopper_INCLUDE_DIRS= \
+# -Dpbcopper_LIBRARIES= \
+
+#get-orig-source:
+# . debian/get-orig-source
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/watch b/debian/watch
new file mode 100644
index 0000000..5d88692
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,39 @@
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php #PACKAGE#-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/#PACKAGE#-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/#PACKAGE#-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge
+# http://sf.net/#PACKAGE#/#PACKAGE#-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+
+# Uncomment to find new files on Github
+# - when using releases:
+# https://github.com/#GITHUBUSER#/#PACKAGE#/releases .*/archive/#PREFIX#(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+# - when using tags
+# https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
+# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible
+
+# PyPi repository of Python modules
+# see https://lists.debian.org/debian-python/2015/02/msg00027.html
+# http://pypi.debian.net/#module#/#module#-(.+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
+# Bitbucket
+# https://bitbucket.org/<user>/<project>/downloads .*/(\d\S*)\.tar\.gz
+
+# Gitlab
+# opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/<project>-$1\.tar\.gz/g \
+# https://gitlab.com/<user>/<project>/tags .*archive\.tar\.gz\?ref=v?(\d\S*)
+
+# if tweaking of source is needed
+# \
+# debian debian/get-orig-source
+
+# if you need to repack and choose +dfsg prefix
+# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \
--
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