[med-svn] [hinge] 04/04: Initial packaging
Afif Elghraoui
afif at moszumanska.debian.org
Tue May 23 05:08:10 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository hinge.
commit d63a850f689be69987dc0e765ef5f230e835e662
Author: Afif Elghraoui <afif at debian.org>
Date: Tue May 23 00:59:25 2017 -0400
Initial packaging
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 38 +++++++++
debian/copyright | 161 +++++++++++++++++++++++++++++++++++
debian/docs | 2 +
debian/patches/external-spdlog.patch | 58 +++++++++++++
debian/patches/series | 1 +
debian/rules | 5 ++
debian/source/format | 1 +
debian/upstream/metadata | 9 ++
debian/watch | 5 ++
11 files changed, 286 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..605da43
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+hinge (0.42-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at debian.org> Thu, 07 Jul 2016 03:07:30 -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..f2042af
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,38 @@
+Source: hinge
+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),
+ cmake,
+ libspdlog-dev,
+ libboost-dev,
+ libboost-graph-dev,
+ libhdf5-dev,
+ zlib1g-dev,
+ pandoc,
+Standards-Version: 3.9.8
+Homepage: https://github.com/fxia22/HINGE
+Vcs-Git: https://anonscm.debian.org/git/debian-med/hinge.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/hinge.git
+
+Package: hinge
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ daligner,
+ dazzdb,
+ dascrubber,
+# dextractor,
+ python-numpy,
+ python-ujson,
+ python-configparser,
+# python-colormap,
+# python-easydev,
+ python-pbcore,
+ python-networkx,
+ python-matplotlib,
+Description: long read assembler based on an idea called hinging
+ HINGE is an OLC(Overlap-Layout-Consensus) assembler.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ecf2e19
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,161 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: hinge
+Upstream-Contact: Fei Xia <xf1280 at gmail.com>
+Source: https://github.com/HingeAssembler/HINGE
+Files-Excluded: binary
+
+Files: *
+Copyright: 2016 Govinda Kamath
+ 2016 Fei Xia
+ 2016 Ilan Shomorony
+ 2016 Thomas Courtade
+ 2016 David Tse
+License: BSD-3-Clause/HINGE
+
+Files:
+ src/include/paf.h
+ src/include/paf.c
+ src/include/kseq.h
+Copyright: 2008-2009, 2011 Attractive Chaos <attractor at live.co.uk>
+License: MIT
+
+Files:
+ src/include/align.h
+ src/include/align.c
+ src/include/QV.h
+ src/include/DB.h
+Copyright: 2014 Eugene W Myers Jr <gene.myers at gmail.com>
+License: BSD-3-Clause/EWM
+
+Files: src/include/cmdline.h
+Copyright: 2009 Hideyuki Tanaka
+License: BSD-3-Clause
+
+Files:
+ src/include/common.h
+ src/lib/falcon.c
+ src/lib/kmer_lookup.c
+ src/lib/DW_banded.c
+Copyright: 2011-2014 Pacific Biosciences of California
+License: BSD-3-Clause/PacBio
+
+Files: debian/*
+Copyright: 2017 Afif Elghraoui <afif at debian.org>
+License: BSD-3-Clause
+
+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:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * 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.
+ * Neither the name of the <organization> 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 <copyright holder> ''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 <copyright holder> 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/EWM
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ · Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ · 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.
+ · The name of EWM may not be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY EWM ”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 EWM 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/HINGE
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ · Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ · 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.
+ · The name of HINGE may not be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY Govinda Kamath, Fei Xia, Ilan Shomorony, Thomas
+ Courtade and David Tse ”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 Govinda
+ Kamath, Fei Xia, Ilan Shomorony, Thomas Courtade, and David Tse 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/PacBio
+ 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:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * 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.
+ * 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: 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..b36bce1
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README.md
+parameter_description.md
diff --git a/debian/patches/external-spdlog.patch b/debian/patches/external-spdlog.patch
new file mode 100644
index 0000000..9479223
--- /dev/null
+++ b/debian/patches/external-spdlog.patch
@@ -0,0 +1,58 @@
+Description: Exclude build directory for spdlog
+ remove subdir declaration from src/CMakeLists.txt and:
+ sed -i s/spdlog// src/{consensus,layout,filter,maximal}/CMakeLists.txt
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2017-05-23
+--- hinge.orig/src/CMakeLists.txt
++++ hinge/src/CMakeLists.txt
+@@ -29,8 +29,6 @@
+
+ add_subdirectory(lib lib)
+
+-add_subdirectory(spdlog)
+-
+ #add_subdirectory(ogdf)
+
+ find_program(PANDOC pandoc)
+--- hinge.orig/src/consensus/CMakeLists.txt
++++ hinge/src/consensus/CMakeLists.txt
+@@ -1,7 +1,7 @@
+ cmake_minimum_required(VERSION 3.2)
+
+ add_executable(draft_assembly draft)
+-target_link_libraries(draft_assembly LAInterface ini falcon spdlog)
++target_link_libraries(draft_assembly LAInterface ini falcon )
+
+ add_executable(consensus consensus.cpp)
+ target_link_libraries(consensus LAInterface falcon ini)
+--- hinge.orig/src/filter/CMakeLists.txt
++++ hinge/src/filter/CMakeLists.txt
+@@ -1,6 +1,6 @@
+ cmake_minimum_required(VERSION 3.2)
+
+ add_executable(Reads_filter filter)
+-target_link_libraries(Reads_filter LAInterface ini spdlog)
++target_link_libraries(Reads_filter LAInterface ini )
+
+ install(TARGETS Reads_filter DESTINATION ${libexec})
+--- hinge.orig/src/layout/CMakeLists.txt
++++ hinge/src/layout/CMakeLists.txt
+@@ -6,6 +6,6 @@
+ INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIR} )
+
+ add_executable(hinging hinging)
+-target_link_libraries(hinging LAInterface ini spdlog ${Boost_LIBRARIES})
++target_link_libraries(hinging LAInterface ini ${Boost_LIBRARIES})
+
+ install(TARGETS hinging DESTINATION ${libexec})
+--- hinge.orig/src/maximal/CMakeLists.txt
++++ hinge/src/maximal/CMakeLists.txt
+@@ -1,6 +1,6 @@
+ cmake_minimum_required(VERSION 3.2)
+
+ add_executable(get_maximal_reads maximal)
+-target_link_libraries(get_maximal_reads LAInterface ini spdlog)
++target_link_libraries(get_maximal_reads LAInterface ini )
+
+ install(TARGETS get_maximal_reads DESTINATION ${libexec})
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..4fef5c9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+external-spdlog.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..aee658d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+#export DH_VERBOSE = 1
+
+%:
+ dh $@ --buildsystem=cmake
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..0c7e1e5
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,9 @@
+Reference:
+ Author: Govinda M Kamath and Ilan Shomorony and Fei Xia and Thomas Courtade and David N Tse
+ Title: "HINGE: Long-read assembly achieves optimal repeat resolution"
+ Journal: Genome Research
+ Year: 2017
+ DOI: 10.1101/gr.216465.116
+ PMID: 28320918
+ URL: http://genome.cshlp.org/content/early/2017/03/20/gr.216465.116.abstract
+ eprint: http://genome.cshlp.org/content/early/2017/03/20/gr.216465.116.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..9ead6bb
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%hinge-$1.tar.gz%" \
+ https://github.com/HingeAssembler/HINGE/tags \
+ (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
--
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