[med-svn] [blasr] 02/02: Initial Packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Jul 27 09:33:44 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository blasr.
commit 851176099cd344570dfa20257f7a83138b52ac36
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Jul 27 02:26:01 2015 -0700
Initial Packaging
---
debian/TODO | 5 +++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 23 +++++++++++++++++++++++
debian/copyright | 38 ++++++++++++++++++++++++++++++++++++++
debian/docs | 3 +++
debian/get-orig-source | 39 +++++++++++++++++++++++++++++++++++++++
debian/install | 9 +++++++++
debian/rules | 32 ++++++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 10 ++++++++++
debian/watch | 7 +++++++
12 files changed, 173 insertions(+)
diff --git a/debian/TODO b/debian/TODO
new file mode 100644
index 0000000..a97c396
--- /dev/null
+++ b/debian/TODO
@@ -0,0 +1,5 @@
+* Don't embed libraries in the compiled binaries
+
+* Write/generate man pages
+
+* Add get-orig-source target to d/rules and test the get-orig-source script
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..27cc20d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+blasr (0~20150724+git3ca7fe8-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #793763)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sun, 26 Jul 2015 22:19:06 -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..297701c
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,23 @@
+Source: blasr
+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),
+ python,
+ libhdf5-dev,
+ zlib1g-dev
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/blasr
+Vcs-Git: git://anonscm.debian.org/debian-med/blasr.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/blasr.git
+
+Package: blasr
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: mapping single-molecule sequencing reads
+ Basic local alignment with successive refinement (BLASR) is a method
+ for mapping single-molecule sequencing reads against a reference genome.
+ Such reads are thousands of bases long, with divergence between them
+ and the genome being dominated by insertion and deletion error.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6b8e589
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,38 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: blasr
+Source: https://github.com/PacificBiosciences/blasr
+
+Files: *
+Copyright: 2011-2015 Pacific Biosciences of California, Inc.
+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..0a029f6
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+LICENSES.txt
+README.md
+MANUAL.md
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..e19a66e
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,39 @@
+#!/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
+
+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]\+$/\1/'`
+ git clone --depth 1 --recursive \
+ https://github.com/PacificBiosciences/blasr.git \
+ ../${NAME}-${VERSION}
+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
+
+# Remove useless files
+rm -rf ../${TARDIR}/.git*
+rm -rf ../${TARDIR}/libcpp/.git*
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "../${TARDIR}"
+rm -rf ../${TARDIR}
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..5bc54f4
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,9 @@
+blasr usr/bin
+utils/loadPulses usr/bin
+utils/pls2fasta usr/bin
+utils/samtoh5 usr/bin
+utils/samtom4 usr/bin
+utils/samFilter usr/bin
+utils/toAfg usr/bin
+utils/sawriter usr/bin
+utils/sdpMatcher usr/bin
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..527d645
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,32 @@
+#!/usr/bin/make -f
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+export HDF5_INC=/usr/include/hdf5/serial
+export HDF5_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
+
+# This is needed for libcpp/configure.py. The top-level configure.py
+# uses a command-line argument.
+export NOPBBAM=1
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ ./configure.py --no-pbbam --submodules
+ libcpp/configure.py
+
+override_dh_auto_build:
+ $(MAKE) build-submodule
+ $(MAKE)
+
+# Tests require cram. I don't find it available in Debian
+override_dh_auto_test:
+
+override_dh_auto_clean: override_dh_auto_configure
+ $(MAKE) cleanall
+ # This is created by configure.py
+ rm -f defines.mk
+ # These are created by libcpp/configure.py
+ rm -f libcpp/defines.mk libcpp/pbdata/libconfig.h
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/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..a753685
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+Reference:
+ Author: Mark J Chaisson and Glenn Tesler
+ Title: "Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory"
+ Journal: BMC Bioinformatics
+ Year: 2012
+ Volume: 13
+ Number: 238
+ DOI: 10.1186/1471-2105-13-23
+ PMID: 22988817
+ URL: http://www.biomedcentral.com/1471-2105/13/238
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..f4ce629
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,7 @@
+# Upstream does not assign version numbers for this program. They do,
+# however, create tags for the state that goes along with the SMRT Analysis
+# suite release, but there is no such tag for the most recent one. We're
+# therefore packaging from git-- Upstream installation instructions even
+# direct users to cloning the source repository.
+
+version=3
--
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