[med-svn] [pbgenomicconsensus] 02/05: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Sep 15 08:49:44 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbgenomicconsensus.
commit b20e56ed79693b8c9c8bbad4594483a43789a6bd
Author: Afif Elghraoui <afif at 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 <afif at 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-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at 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: devnet at pacificbiosciences.com
+Source: https://github.com/PacificBiosciences/GenomicConsensus
+
+Files: *
+Copyright: 2011-2015 Pacific Biosciences of California, Inc. <devnet at pacificbiosciences.com>
+License: PacBio-BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at 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
+
--
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