Andreas Tille pushed to branch master at Debian Med / spoa
Commits: f4d7bced by Andreas Tille at 2018-06-09T08:46:04+02:00 Initial packaging - - - - - 9 changed files: - + debian/changelog - + debian/compat - + debian/control - + debian/copyright - + debian/patches/series - + debian/patches/use_debian_packaged_libs.patch - + debian/rules - + debian/source/format - + debian/watch Changes: ===================================== debian/changelog ===================================== --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +spoa (1.1.3-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #xxx) + + -- Andreas Tille <ti...@debian.org> Fri, 08 Jun 2018 13:20:51 +0200 ===================================== debian/compat ===================================== --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +11 ===================================== debian/control ===================================== --- /dev/null +++ b/debian/control @@ -0,0 +1,24 @@ +Source: spoa +Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> +Uploaders: Andreas Tille <ti...@debian.org> +Section: science +Priority: optional +Build-Depends: debhelper (>= 11~), + cmake, + libbioparser-dev +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/med-team/spoa +Vcs-Git: https://salsa.debian.org/med-team/spoa.git +Homepage: https://github.com/rvaser/spoa + +Package: spoa +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: SIMD partial order alignment tool/library + Spoa (SIMD POA) is a c++ implementation of the partial order alignment + (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which + is used to generate consensus sequences (as described in + 10.1093/bioinformatics/btg109). It supports three alignment modes: local + (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment + (overlap). ===================================== debian/copyright ===================================== --- /dev/null +++ b/debian/copyright @@ -0,0 +1,31 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Spoa +Upstream-Contact: +Source: https://github.com/rvaser/spoa/releases + +Files: * +Copyright: 2016-2018 Robert Vaser +License: MIT + +Files: debian/* +Copyright: 2018 Andreas Tille <ti...@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. ===================================== debian/patches/series ===================================== --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +use_debian_packaged_libs.patch ===================================== debian/patches/use_debian_packaged_libs.patch ===================================== --- /dev/null +++ b/debian/patches/use_debian_packaged_libs.patch @@ -0,0 +1,31 @@ +Author: Andreas Tille <ti...@debian.org> +Last-Update: Fri, 08 Jun 2018 13:20:51 +0200 +Description: Use Debian packaged libraries + +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -45,11 +45,7 @@ if (spoa_build_executable) + src/sequence.cpp + src/main.cpp) + +- if (NOT TARGET bioparser) +- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) +- endif() +- +- target_link_libraries(spoa_bin spoa bioparser) ++ target_link_libraries(spoa_bin spoa) + set_target_properties(spoa_bin PROPERTIES OUTPUT_NAME spoa) + + install(TARGETS spoa_bin DESTINATION ${CMAKE_INSTALL_BINDIR}) +@@ -66,10 +62,5 @@ if (spoa_build_tests) + src/sequence.cpp + test/spoa_test.cpp) + +- if (NOT TARGET bioparser) +- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) +- endif() +- add_subdirectory(vendor/googletest/googletest EXCLUDE_FROM_ALL) +- +- target_link_libraries(spoa_test spoa bioparser gtest_main) ++ target_link_libraries(spoa_test spoa ) + endif(spoa_build_tests) ===================================== debian/rules ===================================== --- /dev/null +++ b/debian/rules @@ -0,0 +1,22 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 +export LC_ALL=C.UTF-8 + +include /usr/share/dpkg/default.mk +# this provides: +# DEB_SOURCE: the source package name +# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision) +# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision +# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch +# DEB_VERSION_UPSTREAM: the package's upstream version +# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog + +# for hardening you might like to uncomment this: +# export DEB_BUILD_MAINT_OPTIONS=hardening=+all + +%: + dh $@ + +#get-orig-source: +# . debian/get-orig-source ===================================== debian/source/format ===================================== --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) ===================================== debian/watch ===================================== --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=4 + +https://github.com/rvaser/spoa/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/spoa/commit/f4d7bced6ad06bba929aeb50b124f9cc74cf61d9 -- View it on GitLab: https://salsa.debian.org/med-team/spoa/commit/f4d7bced6ad06bba929aeb50b124f9cc74cf61d9 You're receiving this email because of your account on salsa.debian.org.
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