[med-svn] [pbbam] 02/02: Rough draft packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Sep 6 22:24:13 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbbam.
commit 48d2036c0b67f0803fb2a1c64b48a1157ac69886
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun Sep 6 15:18:22 2015 -0700
Rough draft packaging
---
debian/README.source | 10 ++++
debian/TODO | 2 +
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 32 ++++++++++
debian/copyright | 126 +++++++++++++++++++++++++++++++++++++++
debian/docs | 0
debian/patches/series | 1 +
debian/patches/set-samtools-path | 15 +++++
debian/rules | 19 ++++++
debian/source/format | 1 +
11 files changed, 212 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..c29c516
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+pbbam for Debian
+----------------
+
+* The swig bindings require a version of swig higher than 3.0.2 (currently in unstable).
+ Without this, python and R bindings cannot be built.
+
+
+
+ -- Afif Elghraoui <afif at ghraoui.name>, Sun, 6 Sep 2015 13:57:45 -0700
+
diff --git a/debian/TODO b/debian/TODO
new file mode 100644
index 0000000..4677856
--- /dev/null
+++ b/debian/TODO
@@ -0,0 +1,2 @@
+* Fix package names and sections
+* Fix source version (it's 0.1.0-- see CHANGELOG.md)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..3567dbe
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pbbam (0~20150813+git4e9e417-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #798220)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sun, 06 Sep 2015 11:46:40 -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..c5d8ede
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,32 @@
+Source: pbbam
+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),
+ cmake,
+# swig3.0,
+ doxygen,
+ libboost-dev (>= 1.54),
+ zlib1g-dev,
+ libhts-dev,
+ samtools
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/pbbam
+Vcs-Git: git://anonscm.debian.org/debian-med/pbbam.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/pbbam.git
+
+Package: libpbbam
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Pacific Biosciences binary alignment/map (BAM) library
+ The BAM format is a binary, compressed, record-oriented container format
+ for raw or aligned sequence reads. The associated SAM format is a text
+ representation of the same data. The specifications for BAM/SAM are maintained
+ by the SAM/BAM Format Specification Working Group.
+ .
+ PacBio-produced BAM files are fully compatible with the BAM specification,
+ but makes use of the extensibility mechanisms of the BAM specification to
+ encode PacBio-specific information. The pbbam library provides tools to
+ work with these files
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7fd54cb
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,126 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pbbam
+Upstream-Contact: Pacific Biosciences <devnet at pacificbiosciences.com>
+Source: https://github.com/PacificBiosciences/pbbam
+
+Files: *
+Copyright: 2014-2015 Pacific Biosciences of California, Inc. <devnet at pacificbiosciences.com>
+License: PacBio-BSD-3-Clause
+
+# Probably want to exclude these files since they don't appear to be necessary
+Files: cmake/*
+Copyright: 2006-2010 Mathieu Malaterre <mathieu.malaterre at gmail.com>
+License: ?
+
+Files: src/pugixml/*
+Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine at gmail.com>
+ 2003 Kristen Wegner <kristen at tima.net>
+License: MIT
+
+Files: tools/pbindex/src/OptionParser.*
+Copyright: 2010 Johannes Weißl <jargon at molb.org>
+License: BSD-3-Clause or BSD-2-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 (subject to the limitations in the
+ disclaimer below) 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.
+
+License: 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 the University nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 THE HOLDERS OR
+ 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.
+
+License: BSD-2-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.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 THE
+ COPYRIGHT HOLDER OR 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.
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following
+ conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e69de29
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..1a37804
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+set-samtools-path
diff --git a/debian/patches/set-samtools-path b/debian/patches/set-samtools-path
new file mode 100644
index 0000000..aa1819f
--- /dev/null
+++ b/debian/patches/set-samtools-path
@@ -0,0 +1,15 @@
+Description: Set samtools path
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-09-06
+--- pbbam.orig/tests/CMakeLists.txt
++++ pbbam/tests/CMakeLists.txt
+@@ -2,7 +2,7 @@
+
+ # find samtools binary for comparing against 'gold standard' files
+ #set(Samtools_Dir "/Users/derek/development/samtools")
+-set(Samtools_Dir "${PacBioBAM_RootDir}/../../../../prebuilt.out/samtools/samtools-0.1.19/ubuntu-1404/bin")
++set(Samtools_Dir "")
+ find_program(Samtools_Bin samtools HINTS ${Samtools_Dir})
+
+ # ensure tests directory exists
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1a9b4a7
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,19 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+%:
+ dh $@ --parallel
+
+override_dh_auto_configure:
+ dh_auto_configure -- \
+ -DPacBioBAM_build_shared=ON \
+ -DPacBioBAM_build_tests=OFF \
+ -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \
+ -DHTSLIB_INCLUDE_DIRS=/usr/include \
+ -DHTSLIB_LIBRARIES=/usr/lib
+# -DPacBioBAM_wrap_python=ON \
+# -DPacBioBAM_wrap_r=ON
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)
--
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