Date: Tue, 19 Jan 2021 07:56:50 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r562033 - in head/biology: . bioparser Message-ID: <202101190756.10J7uoa7003935@repo.freebsd.org>
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Author: yuri Date: Tue Jan 19 07:56:49 2021 New Revision: 562033 URL: https://svnweb.freebsd.org/changeset/ports/562033 Log: New port: biology/bioparser: C++ header only parsing library for several formats in bioinformatics Added: head/biology/bioparser/ head/biology/bioparser/Makefile (contents, props changed) head/biology/bioparser/distinfo (contents, props changed) head/biology/bioparser/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Jan 19 07:54:17 2021 (r562032) +++ head/biology/Makefile Tue Jan 19 07:56:49 2021 (r562033) @@ -12,6 +12,7 @@ SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa + SUBDIR += bioparser SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 Added: head/biology/bioparser/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioparser/Makefile Tue Jan 19 07:56:49 2021 (r562033) @@ -0,0 +1,39 @@ +# $FreeBSD$ + +PORTNAME= bioparser +DISTVERSION= 3.0.12 +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ header only parsing library for several formats in bioinformatics + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +TEST_DEPENDS= googletest>0:devel/googletest + +USES= cmake + +USE_GITHUB= yes +GH_ACCOUNT= rvaser +GH_TUPLE= rvaser:biosoup:e2b39f1:biosoup/vendor/biosoup + +NO_ARCH= yes + +PLIST_FILES= include/bioparser/fasta_parser.hpp \ + include/bioparser/fastq_parser.hpp \ + include/bioparser/mhap_parser.hpp \ + include/bioparser/paf_parser.hpp \ + include/bioparser/parser.hpp \ + include/bioparser/sam_parser.hpp + +do-install: + cd ${WRKSRC}/include && ${COPYTREE_SHARE} ${PORTNAME} ${STAGEDIR}${PREFIX}/include + +do-test: + @cd ${BUILD_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -Dbioparser_build_tests:BOOL=ON ${CMAKE_SOURCE_PATH} && \ + ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ + ${BUILD_WRKSRC}/bin/bioparser_test + +.include <bsd.port.mk> Added: head/biology/bioparser/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioparser/distinfo Tue Jan 19 07:56:49 2021 (r562033) @@ -0,0 +1,5 @@ +TIMESTAMP = 1611042654 +SHA256 (rvaser-bioparser-3.0.12_GH0.tar.gz) = 00672e3dfa4946c37df8818d283742b51f21c8a0c70ddac543b241d6ba54dbcb +SIZE (rvaser-bioparser-3.0.12_GH0.tar.gz) = 1013329 +SHA256 (rvaser-biosoup-e2b39f1_GH0.tar.gz) = fe122e65d1691ca781584d8bb42538c5904852ccbb1ec48bc13aa2652b0f9ddc +SIZE (rvaser-biosoup-e2b39f1_GH0.tar.gz) = 6979 Added: head/biology/bioparser/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioparser/pkg-descr Tue Jan 19 07:56:49 2021 (r562033) @@ -0,0 +1,4 @@ +Bioparser is a C++ header only parsing library for several formats in +bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files. + +WWW: https://github.com/rvaser/bioparser
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