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Bacon" Date: Mon, 23 Apr 2018 16:23:53 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r468101 - in head/biology: . pbcopper pbcopper/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . pbcopper pbcopper/files X-SVN-Commit-Revision: 468101 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 23 Apr 2018 16:23:54 -0000 Author: jwb Date: Mon Apr 23 16:23:53 2018 New Revision: 468101 URL: https://svnweb.freebsd.org/changeset/ports/468101 Log: biology/pbcopper: Core C++ library for Pacific Biosciences tools Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15171 Added: head/biology/pbcopper/ head/biology/pbcopper/Makefile (contents, props changed) head/biology/pbcopper/distinfo (contents, props changed) head/biology/pbcopper/files/ head/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake (contents, props changed) head/biology/pbcopper/pkg-descr (contents, props changed) head/biology/pbcopper/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Apr 23 16:08:21 2018 (r468100) +++ head/biology/Makefile Mon Apr 23 16:23:53 2018 (r468101) @@ -82,6 +82,7 @@ SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam + SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap Added: head/biology/pbcopper/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbcopper/Makefile Mon Apr 23 16:23:53 2018 (r468101) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= pbcopper +DISTVERSION= g20180413 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Core C++ library for Pacific Biosciences tools + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +LIB_DEPENDS= libboost_regex.so:devel/boost-libs + +USES= cmake +# Although there are a couple releases, git describe --tags does not work +# so we cannot use the usual USE_GITHUB tools here. +USE_GITHUB= yes +GH_ACCOUNT= PacificBiosciences +GH_TAGNAME= 17ef457a0dbe1894a8d17af7ddba01a6261bf117 + +do-install: + ${INSTALL_DATA} ${BUILD_WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib + cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include + ${MV} ${STAGEDIR}${PREFIX}/include/meson.build \ + ${STAGEDIR}${PREFIX}/include/pbcopper + +.include Added: head/biology/pbcopper/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbcopper/distinfo Mon Apr 23 16:23:53 2018 (r468101) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524500014 +SHA256 (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 13f006d53334a0538657e0ba5c6e02f811f1901cd25fce220fc9011726ffe23f +SIZE (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 3033636 Added: head/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake Mon Apr 23 16:23:53 2018 (r468101) @@ -0,0 +1,21 @@ +--- cmake/pbcopper-gitsha1.cmake.orig 2018-03-16 16:16:38 UTC ++++ cmake/pbcopper-gitsha1.cmake +@@ -5,16 +5,15 @@ endif() + set(__find_git_sha1 YES) + + function(find_git_sha1 _GIT_SHA1) +- find_package(Git QUIET REQUIRED) + execute_process(COMMAND +- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*" ++ echo ce9a4b6 + WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" + RESULT_VARIABLE res + OUTPUT_VARIABLE out + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if (NOT res EQUAL 0) +- message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`") ++ message(FATAL_ERROR "Could not determine git sha1") + endif() + set(${_GIT_SHA1} "${out}" PARENT_SCOPE) + endfunction() Added: head/biology/pbcopper/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbcopper/pkg-descr Mon Apr 23 16:23:53 2018 (r468101) @@ -0,0 +1,5 @@ +The pbcopper library provides a suite of data structures, algorithms, and +utilities for C++ applications. It is a core component of Pacific Biosciences +genomics analysis tools. + +WWW: https://github.com/PacificBiosciences/pbcopper Added: head/biology/pbcopper/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbcopper/pkg-plist Mon Apr 23 16:23:53 2018 (r468101) @@ -0,0 +1,75 @@ +include/pbcopper/PbcopperConfig.h +include/pbcopper/align/Seed.h +include/pbcopper/align/Seeds.h +include/pbcopper/align/internal/Seed-inl.h +include/pbcopper/align/internal/Seeds-inl.h +include/pbcopper/cli/CLI.h +include/pbcopper/cli/HelpPrinter.h +include/pbcopper/cli/Interface.h +include/pbcopper/cli/Option.h +include/pbcopper/cli/OptionFlags.h +include/pbcopper/cli/Parser.h +include/pbcopper/cli/PositionalArg.h +include/pbcopper/cli/Results.h +include/pbcopper/cli/SingleDashMode.h +include/pbcopper/cli/VersionPrinter.h +include/pbcopper/cli/internal/Option-inl.h +include/pbcopper/cli/toolcontract/Config.h +include/pbcopper/cli/toolcontract/Driver.h +include/pbcopper/cli/toolcontract/InputFileType.h +include/pbcopper/cli/toolcontract/JsonPrinter.h +include/pbcopper/cli/toolcontract/OutputFileType.h +include/pbcopper/cli/toolcontract/ResolvedToolContract.h +include/pbcopper/cli/toolcontract/ResourceType.h +include/pbcopper/cli/toolcontract/Task.h +include/pbcopper/cli/toolcontract/TaskType.h +include/pbcopper/cli/toolcontract/internal/Config-inl.h +include/pbcopper/cli/toolcontract/internal/Driver-inl.h +include/pbcopper/cli/toolcontract/internal/InputFileType-inl.h +include/pbcopper/cli/toolcontract/internal/OutputFileType-inl.h +include/pbcopper/cli/toolcontract/internal/Task-inl.h +include/pbcopper/data/CCSTag.h +include/pbcopper/data/Cigar.h +include/pbcopper/data/CigarOperation.h +include/pbcopper/data/Interval.h +include/pbcopper/data/MovieName.h +include/pbcopper/data/Position.h +include/pbcopper/data/RSMovieName.h +include/pbcopper/data/RSReadName.h +include/pbcopper/data/ReadName.h +include/pbcopper/data/Zmw.h +include/pbcopper/data/internal/CigarOperation-inl.h +include/pbcopper/data/internal/Interval-inl.h +include/pbcopper/data/internal/MovieName-inl.h +include/pbcopper/data/internal/RSMovieName-inl.h +include/pbcopper/data/internal/ReadNameBase-inl.h +include/pbcopper/data/internal/ReadNameBase.h +include/pbcopper/json/JSON.h +include/pbcopper/json/internal/json.hpp +include/pbcopper/logging/Logging.h +include/pbcopper/logging/internal/Logging-inl.h +include/pbcopper/meson.build +include/pbcopper/parallel/FireAndForget.h +include/pbcopper/parallel/WorkQueue.h +include/pbcopper/qgram/Index.h +include/pbcopper/qgram/IndexHit.h +include/pbcopper/qgram/IndexHits.h +include/pbcopper/qgram/internal/Hashing-inl.h +include/pbcopper/qgram/internal/Index-inl.h +include/pbcopper/stream/Stream.h +include/pbcopper/utility/CallbackTimer.h +include/pbcopper/utility/EnumClassHash.h +include/pbcopper/utility/FileUtils.h +include/pbcopper/utility/MoveAppend.h +include/pbcopper/utility/PbcopperVersion.h +include/pbcopper/utility/SafeSubtract.h +include/pbcopper/utility/Stopwatch.h +include/pbcopper/utility/StringUtils.h +include/pbcopper/utility/SystemInfo.h +include/pbcopper/utility/Unused.h +include/pbcopper/utility/internal/CallbackTimer-inl.h +include/pbcopper/utility/internal/FileUtils-inl.h +include/pbcopper/utility/internal/Stopwatch-inl.h +include/pbcopper/utility/internal/StringUtils-inl.h +include/pbcopper/utility/internal/SystemInfo-inl.h +lib/libpbcopper.a