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commit b20e56ed79693b8c9c8bbad4594483a43789a6bd Author: Afif Elghraoui <a...@ghraoui.name> Date: Mon Sep 14 23:35:45 2015 -0700 Initial packaging --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ debian/copyright | 39 +++++++++++++++++++++++++++++++++++++++ debian/docs | 1 + debian/rules | 10 ++++++++++ debian/source/format | 1 + debian/watch | 5 +++++ 8 files changed, 110 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..f2e18f2 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +pbgenomicconsensus (1.0.0-1) unstable; urgency=low + + * Initial release (Closes: #787977) + + -- Afif Elghraoui <a...@ghraoui.name> Mon, 14 Sep 2015 19:17:20 -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..d00c513 --- /dev/null +++ b/debian/control @@ -0,0 +1,48 @@ +Source: pbgenomicconsensus +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> +Uploaders: Afif Elghraoui <a...@ghraoui.name> +Build-Depends: debhelper (>= 9), + dh-python, + python-all, + python-setuptools, + python-pbconsensuscore, + python-pbcore +Standards-Version: 3.9.6 +Homepage: https://github.com/PacificBiosciences/GenomicConsensus +Vcs-Git: git://anonscm.debian.org/debian-med/pbgenomicconsensus.git +Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/pbgenomicconsensus.git + +Package: pbgenomicconsensus +Architecture: all +Depends: ${misc:Depends}, + ${python:Depends}, + python-pbgenomicconsensus +Description: Pacific Biosciences variant and consensus caller + The GenomicConsensus package provides Quiver, Pacific Biosciences' + flagship consensus and variant caller. Quiver is an algorithm that finds + the maximum likelihood template sequence given PacBio reads of the template. + These reads are modeled using a conditional random field approach that + prescribes a probability to a read given a template sequence. In addition to + the base sequence of each read, Quiver uses several additional quality value + covariates that the base caller provides. + . + This package is part of the SMRTAnalysis suite + +Package: python-pbgenomicconsensus +Section: python +Architecture: all +Depends: ${misc:Depends}, + ${python:Depends} +Description: Pacific Biosciences variant and consensus caller (Python 2) + The GenomicConsensus package provides Quiver, Pacific Biosciences' + flagship consensus and variant caller. Quiver is an algorithm that finds + the maximum likelihood template sequence given PacBio reads of the template. + These reads are modeled using a conditional random field approach that + prescribes a probability to a read given a template sequence. In addition to + the base sequence of each read, Quiver uses several additional quality value + covariates that the base caller provides. + . + This package is part of the SMRTAnalysis suite and provides the Python 2 + backend library. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..cef1cd4 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,39 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: GenomicConsensus +Upstream-Contact: dev...@pacificbiosciences.com +Source: https://github.com/PacificBiosciences/GenomicConsensus + +Files: * +Copyright: 2011-2015 Pacific Biosciences of California, Inc. <dev...@pacificbiosciences.com> +License: PacBio-BSD-3-Clause + +Files: debian/* +Copyright: 2015 Afif Elghraoui <a...@ghraoui.name> +License: PacBio-BSD-3-Clause + +License: PacBio-BSD-3-Clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + 3. Neither the name of Pacific Biosciences nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + . + NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE + GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC + BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF + MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS + BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN + IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..b43bf86 --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +README.md diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..8e5def7 --- /dev/null +++ b/debian/rules @@ -0,0 +1,10 @@ +#!/usr/bin/make -f + +#DH_VERBOSE = 1 + +include /usr/share/dpkg/default.mk + +export PYBUILD_NAME := $(DEB_SOURCE) + +%: + LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild 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..ce120b1 --- /dev/null +++ b/debian/watch @@ -0,0 +1,5 @@ +version=3 + +opts="filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/pbgenomicconsensus-$1.tar.gz/" \ + https://github.com/PacificBiosciences/GenomicConsensus/releases (?:.*/)?v?(\d[\d\.]*)\.tar\.gz + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit