[med-svn] [hyphy] 02/02: Initial packaging (moved from svn to git)
Andreas Tille
tille at debian.org
Wed Jul 8 15:50:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository hyphy.
commit e1bf87d8f2f3c2fa4623adad6d31f07bcb9a4df9
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 8 17:28:40 2015 +0200
Initial packaging (moved from svn to git)
---
debian/changelog | 5 ++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 69 +++++++++++++++
debian/copyright | 43 +++++++++
debian/hyphy-common.install | 1 +
debian/hyphy-common.links | 1 +
debian/hyphy-mpi.install | 1 +
debian/hyphy.install | 1 +
debian/patches/arch_all_files_to_usr_share.patch | 16 ++++
debian/patches/series | 2 +
debian/patches/use_debian_sqlite.patch | 108 +++++++++++++++++++++++
debian/rules | 33 +++++++
debian/source/format | 1 +
debian/source/lintian-overrides | 4 +
debian/upstream/metadata | 12 +++
debian/watch | 4 +
17 files changed, 303 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5192a7e
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+hyphy (2.2.4+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 29 Jun 2015 11:13:57 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..7cdbba3
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+gmon.out
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..91faac3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,69 @@
+Source: hyphy
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cmake,
+ mpi-default-dev,
+ libcurl4-gnutls-dev | libcurl4-dev,
+ python,
+ libgtk2.0-dev,
+ libssl-dev,
+ libsqlite3-dev
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/hyphy.git
+Vcs-Git: git://anonscm.debian.org/debian-med/hyphy.git
+Homepage: http://hyphy.org/
+
+Package: hyphy
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ hyphy-common
+Description: Hypothesis testing using Phylogenies
+ HyPhy is an open-source software package for the analysis of genetic
+ sequences using techniques in phylogenetics, molecular evolution, and
+ machine learning. It features a complete graphical user interface (GUI)
+ and a rich scripting language for limitless customization of analyses.
+ Additionally, HyPhy features support for parallel computing environments
+ (via message passing interface) and it can be compiled as a shared
+ library and called from other programming environments such as Python or
+ R. Continued development of HyPhy is currently supported in part by an
+ NIGMS R01 award 1R01GM093939.
+
+Package: hyphy-mpi
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ hyphy-common
+Description: Hypothesis testing using Phylogenies (MPI version)
+ HyPhy is an open-source software package for the analysis of genetic
+ sequences using techniques in phylogenetics, molecular evolution, and
+ machine learning. It features a complete graphical user interface (GUI)
+ and a rich scripting language for limitless customization of analyses.
+ Additionally, HyPhy features support for parallel computing environments
+ (via message passing interface) and it can be compiled as a shared
+ library and called from other programming environments such as Python or
+ R. Continued development of HyPhy is currently supported in part by an
+ NIGMS R01 award 1R01GM093939.
+ .
+ This package provides the MPI version.
+
+Package: hyphy-common
+Architecture: all
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Suggests: hyphy | hyphy-mpi
+Description: Hypothesis testing using Phylogenies (common files)
+ HyPhy is an open-source software package for the analysis of genetic
+ sequences using techniques in phylogenetics, molecular evolution, and
+ machine learning. It features a complete graphical user interface (GUI)
+ and a rich scripting language for limitless customization of analyses.
+ Additionally, HyPhy features support for parallel computing environments
+ (via message passing interface) and it can be compiled as a shared
+ library and called from other programming environments such as Python or
+ R. Continued development of HyPhy is currently supported in part by an
+ NIGMS R01 award 1R01GM093939.
+ .
+ This package provides files that are common to all binary versions.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..136d6c1
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,43 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Spencer V. Muse <muse at stat.ncsu.edu>
+Upstream-Name: HyPhy
+Source: https://github.com/veg/hyphy/releases
+Files-Excluded: installers
+ CMakeWin32
+ */SQLite*
+ .gitignore
+ */.DS_Store
+ */.xvpics
+ */.gtkrc.swp
+
+Files: *
+Copyright: 1997-2015 Sergei L Kosakovsky Pond <spond at ucsd.edu>
+ Simon D. W. Frost,
+ Spencer V. Muse <muse at stat.ncsu.edu>
+ and others
+License: MIT
+
+Files: debian/*
+Copyright: © 2015 Andreas Tille <tille at debian.org>
+License: MIT
+
+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/hyphy-common.install b/debian/hyphy-common.install
new file mode 100644
index 0000000..96552d8
--- /dev/null
+++ b/debian/hyphy-common.install
@@ -0,0 +1 @@
+usr/lib/* usr/share
diff --git a/debian/hyphy-common.links b/debian/hyphy-common.links
new file mode 100644
index 0000000..e603a97
--- /dev/null
+++ b/debian/hyphy-common.links
@@ -0,0 +1 @@
+usr/share/hyphy usr/lib/hyphy
diff --git a/debian/hyphy-mpi.install b/debian/hyphy-mpi.install
new file mode 100644
index 0000000..08188b9
--- /dev/null
+++ b/debian/hyphy-mpi.install
@@ -0,0 +1 @@
+usr/bin/*mpi
diff --git a/debian/hyphy.install b/debian/hyphy.install
new file mode 100644
index 0000000..df8f9bb
--- /dev/null
+++ b/debian/hyphy.install
@@ -0,0 +1 @@
+usr/bin/*gtk
diff --git a/debian/patches/arch_all_files_to_usr_share.patch b/debian/patches/arch_all_files_to_usr_share.patch
new file mode 100644
index 0000000..c840d6f
--- /dev/null
+++ b/debian/patches/arch_all_files_to_usr_share.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 29 Jun 2015 11:13:57 +0200
+Description: Move arch all files to /usr/share
+ Deactivated since it does not work this way
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -277,7 +277,7 @@ target_link_libraries(hyphy_mp ${DEFAULT
+
+ install(
+ TARGETS hyphy_mp
+- LIBRARY DESTINATION lib
++ LIBRARY DESTINATION share
+ OPTIONAL
+ )
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..88e398d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+# arch_all_files_to_usr_share.patch
+use_debian_sqlite.patch
diff --git a/debian/patches/use_debian_sqlite.patch b/debian/patches/use_debian_sqlite.patch
new file mode 100644
index 0000000..6e4cd7c
--- /dev/null
+++ b/debian/patches/use_debian_sqlite.patch
@@ -0,0 +1,108 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 29 Jun 2015 11:13:57 +0200
+Description: Use Debian packaged sqlite3
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -179,6 +179,36 @@ if(${CURL_FOUND})
+ endif(${CURL_FOUND})
+
+ #-------------------------------------------------------------------------------
++# check for Debian packaged sqlite
++# stolen from https://sources.debian.net/src/u1db/13.10-6/debian/patches/fix_linking/?hl=103
++#-------------------------------------------------------------------------------
++find_package(PkgConfig)
++pkg_check_modules(PC_SQLITE3 sqlite3)
++
++find_path(SQLITE3_INCLUDE_DIR sqlite3.h
++ HINTS
++ ${PC_SQLITE3_INCLUDE_DIRS}
++ /usr/include
++ /usr/local/include
++ /opt/local/include
++)
++
++find_library(SQLITE3_LIBRARY
++ NAMES ${SQLITE3_NAMES} libsqlite3.so libsqlite3.a
++ HINTS ${PC_SQLITE3_LIBRARY_DIRS}
++ /usr/lib /usr/local/lib /opt/local/lib
++)
++
++include(FindPackageHandleStandardArgs)
++find_package_handle_standard_args(SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
++
++if(SQLITE3_FOUND)
++ # set(SQLITE3_LIBRARIES ${SQLITE3_LIBRARY})
++ set(DEFAULT_LIBRARIES dl pthread crypto curl ssl sqlite3)
++ set(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})
++endif()
++
++#-------------------------------------------------------------------------------
+ # gtest dependency
+ #-------------------------------------------------------------------------------
+ add_subdirectory(contrib/gtest-1.7.0)
+@@ -211,13 +241,12 @@ file(GLOB SRC_NEW src/new/*.cpp)
+
+ set(SRC_LINK src/lib/Link/THyPhy.cpp)
+ set(SRC_PREFS src/gui/preferences.cpp)
+-set(SRC_SQLITE3 contrib/SQLite-3.8.2/sqlite3.c)
+ set(SRC_UNIXMAIN src/mains/unix.cpp)
+ set(SRC_GTKMAIN src/mains/gtk.cpp)
+ set(SRC_MACMAIN src/mains/mac.cpp)
+ set(SRC_UTILS src/utils/hyphyunixutils.cpp)
+
+-set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS})
++set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_UTILS})
+
+
+ #-------------------------------------------------------------------------------
+@@ -229,11 +258,6 @@ set_property(
+ )
+
+ set_property(
+- SOURCE ${SRC_SQLITE3}
+- PROPERTY COMPILE_FLAGS "-Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
+-)
+-
+-set_property(
+ SOURCE src/core/calcnode2.cpp
+ PROPERTY COMPILE_FLAGS "-fstrict-aliasing -funroll-loops"
+ )
+@@ -250,7 +274,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+ include_directories(
+ src/core/include
+ src/lib/Link src/new/include
+- contrib/SQLite-3.8.2 # SQLite
+ src/gui/include
+ src/gui/include/Components
+ src/gui/include/WindowClasses
+@@ -438,11 +461,11 @@ set_target_properties(
+ LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
+ )
+
++
+ #-------------------------------------------------------------------------------
+ # hyphy gtk+ target
+ #-------------------------------------------------------------------------------
+
+-
+ find_package(GTK2 2.6)
+
+ if((${GTK2_FOUND}))
+@@ -454,6 +477,7 @@ if((${GTK2_FOUND}))
+ )
+ include_directories(
+ ${GTK2_INCLUDE_DIRS}
++ ${SQLITE3_INCLUDE_DIRS}
+ src/gui/gtk/include
+ src/gui/gtk/include/Components
+ /Developer/Headers/FlatCarbon
+@@ -544,7 +568,7 @@ if(APPLE AND NOT ${MACOSX_GT_LION})
+ add_executable(HyPhy
+ MACOSX_BUNDLE
+ EXCLUDE_FROM_ALL
+- ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_GUI} ${SRC_MACGUI} ${SRC_MACMAIN}
++ ${SRC_CORE} ${SRC_NEW} ${SRC_GUI} ${SRC_MACGUI} ${SRC_MACMAIN}
+ ${RES_MACGUI}
+ )
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c7e007d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@ --buildsystem=cmake
+
+override_dh_auto_configure:
+ dh_auto_configure -- -DINSTALL_PREFIX=/usr
+
+override_dh_auto_build:
+ dh_auto_build -- HYPHYGTK MPI GTEST
+ # LIB no idea about the purpose of the dynamic library - executables are not simply linked against it
+
+override_dh_auto_test:
+ ./obj-$(DEB_TARGET_GNU_TYPE)/HYPHYGTEST
+
+override_dh_install:
+ # smallcaps for executables
+ for bindir in `find . -type d -name bin` ; do \
+ for bin in $${bindir}/* ; do \
+ # ln -s `basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
+ mv $${bindir}/`basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
+ done ; \
+ done
+ dh_install
+ # remove some junk that should not even be in the source tarball
+ find debian -name .DS_Store -delete
+ find debian -name .xvpics -exec rm '{}' ';'
+ find debian -name .gtkrc.swp -delete
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
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/source/lintian-overrides b/debian/source/lintian-overrides
new file mode 100644
index 0000000..9b9835c
--- /dev/null
+++ b/debian/source/lintian-overrides
@@ -0,0 +1,4 @@
+# These files are not used anyway
+hyphy source: outdated-autotools-helper-file contrib/gtest-1.7.0/build-aux/config.sub 2012-02-10
+hyphy source: outdated-autotools-helper-file contrib/gtest-1.7.0/build-aux/config.guess 2012-02-10
+
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..999b729
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Sergei L. Kosakovsky Pond and Simon D. W. Frost and Spencer V. Muse
+ Title: "HyPhy: hypothesis testing using phylogenies"
+ Journal: Bioinformatics
+ Year: 2005
+ Volume: 21
+ Number: 5
+ Pages: 676-679
+ DOI: 10.1093/bioinformatics/bti079
+ PMID: 15509596
+ URL: http://bioinformatics.oxfordjournals.org/content/21/5/676.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/21/5/676.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..03a52b2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ https://github.com/veg/hyphy/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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