[med-svn] [consensuscore2] 02/09: Initial packaging that seems to work.
Afif Elghraoui
afif at moszumanska.debian.org
Mon Jul 4 01:31:26 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository consensuscore2.
commit d4f9045fbc48e125a40c4d305375bd5b46607f6b
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun Jul 3 15:29:39 2016 -0700
Initial packaging that seems to work.
---
debian/changelog | 6 +++
debian/compat | 1 +
debian/control | 73 ++++++++++++++++++++++++++++++++++++
debian/libconsensuscore2-dev.install | 3 ++
debian/patches/build.patch | 18 +++++++++
debian/patches/series | 1 +
debian/rules | 36 ++++++++++++++++++
debian/source/format | 1 +
debian/watch | 4 ++
9 files changed, 143 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..986a249
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+consensuscore2 (0.11.0-1) unstable; urgency=medium
+
+ * Initial release (Closes: #nnnn)
+ (0.11.0 based on git 841b340 - 2016-05-04)
+
+ -- Afif Elghraoui <afif at debian.org> Fri, 15 Apr 2016 21:05:21 -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..787802a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,73 @@
+Source: consensuscore2
+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,
+ dh-exec,
+ cmake,
+ swig,
+ libboost-dev,
+# Python2
+ python-all,
+ python-all-dev,
+ python-setuptools,
+ python-numpy (>= 1.6.0),
+# Python3
+ python3-all,
+ python3-all-dev,
+ python3-setuptools,
+ python3-numpy (>= 1.6.0),
+Standards-Version: 3.9.8
+Homepage: https://github.com/PacificBiosciences/ConsensusCore2
+Vcs-Git: https://anonscm.debian.org/git/debian-med/consensuscore2.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/consensuscore2.git
+
+Package: libconsensuscore2-dev
+Section: libdevel
+Architecture: any-amd64 any-i386
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Description: generate consensus sequences for PacBio data -- development files
+ ConsensusCore2 embodies core C++ routines underlying the Arrow HMM
+ algorithm for PacBio multi-sequence consensus. Arrow is the successor
+ to the Quiver model---a CRF model that was embodied in the
+ ConsensusCore C++ library. Compared to Quiver, the Arrow model is more
+ statistically principled and easier and more robust to train.
+ .
+ This package installs the headers and static library.
+
+Package: python-consensuscore2
+Section: python
+Architecture: any-amd64 any-i386
+Depends:
+ ${python:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends},
+Description: generate consensus sequences for PacBio data -- Python 2
+ ConsensusCore2 embodies core C++ routines underlying the Arrow HMM
+ algorithm for PacBio multi-sequence consensus. Arrow is the successor
+ to the Quiver model---a CRF model that was embodied in the
+ ConsensusCore C++ library. Compared to Quiver, the Arrow model is more
+ statistically principled and easier and more robust to train.
+ .
+ This package installs the library for Python 2.
+
+Package: python3-consensuscore2
+Section: python
+Architecture: any-amd64 any-i386
+Depends:
+ ${python3:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends},
+Description: generate consensus sequences for PacBio data -- Python 3
+ ConsensusCore2 embodies core C++ routines underlying the Arrow HMM
+ algorithm for PacBio multi-sequence consensus. Arrow is the successor
+ to the Quiver model---a CRF model that was embodied in the
+ ConsensusCore C++ library. Compared to Quiver, the Arrow model is more
+ statistically principled and easier and more robust to train.
+ .
+ This package installs the library for Python 3.
diff --git a/debian/libconsensuscore2-dev.install b/debian/libconsensuscore2-dev.install
new file mode 100755
index 0000000..8829a4f
--- /dev/null
+++ b/debian/libconsensuscore2-dev.install
@@ -0,0 +1,3 @@
+#!/usr/bin/dh-exec
+lib/libpbconsensus.a /usr/lib/${DEB_HOST_MULTIARCH}
+include /usr
diff --git a/debian/patches/build.patch b/debian/patches/build.patch
new file mode 100644
index 0000000..00725ca
--- /dev/null
+++ b/debian/patches/build.patch
@@ -0,0 +1,18 @@
+Description: Don't use Git to determine upstream version
+ We are not in the upstream's git repository for this to work.
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-07-03
+--- consensuscore2.orig/CMakeLists.txt
++++ consensuscore2/CMakeLists.txt
+@@ -24,10 +24,7 @@
+
+ file(MAKE_DIRECTORY ${PacBioConsensus_LibDir})
+
+-# find the git sha1
+ list(APPEND CMAKE_MODULE_PATH "${PacBioConsensus_RootDir}/cmake")
+-include(FindGitSha1)
+-find_git_sha1(CC2_GIT_SHA1)
+
+ configure_file(
+ ${PacBioConsensus_IncludeDir}/pacbio/consensus/Version.h.in
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..5879227
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+build.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6a2bb41
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,36 @@
+#!/usr/bin/make -f
+
+#export DH_VERBOSE = 1
+export LC_ALL=C.UTF-8
+
+export PYBUILD_NAME=consensuscore2
+
+%:
+ dh $@ --with python2,python3 --buildsystem=pybuild
+
+# The python packages need to be installed as soon as they're built,
+# otherwise, changing the version will overwrite the previous attempt.
+define finalize
+dh_auto_configure --package=$1
+dh_auto_build --package=$1
+dh_auto_install --package=$1
+endef
+
+# Configuration and build is done in one step.
+override_dh_auto_configure:
+
+override_dh_auto_build:
+ $(call $(finalize),python-consensuscore2)
+ $(call $(finalize),python3-consensuscore2)
+# The static library is already built at this point.
+
+override_dh_auto_clean:
+ dh_auto_clean --buildsystem=cmake
+ $(RM) include/pacbio/consensus/Version.h
+ $(RM) swig/ConsensusCore2.i
+ $(RM) lib/libpbconsensus.a
+
+override_dh_clean:
+ dh_clean -O--buildsystem=cmake
+
+override_dh_auto_test:
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..16acfee
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+# Upstream does not tag releases.
+# Their Git history has to be manually inspected for milestone commits.
--
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