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| author | Yuri Victorovich <yuri@FreeBSD.org> | 2021-01-19 07:56:49 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2021-01-19 07:56:49 +0000 |
| commit | 352da80b910140aee34b4869d47467e8a18aa777 (patch) | |
| tree | a52cf83a5b62a2279ec72de9ee126f04f6d41975 /biology | |
| parent | d542114626269386a9b8823746e5a157813332da (diff) | |
| download | ports-352da80b910140aee34b4869d47467e8a18aa777.tar.gz ports-352da80b910140aee34b4869d47467e8a18aa777.zip | |
New port: biology/bioparser: C++ header only parsing library for several formats in bioinformatics
Notes
Notes:
svn path=/head/; revision=562033
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/bioparser/Makefile | 39 | ||||
| -rw-r--r-- | biology/bioparser/distinfo | 5 | ||||
| -rw-r--r-- | biology/bioparser/pkg-descr | 4 |
4 files changed, 49 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 24eca15ba05c..bfdf4a46405b 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -12,6 +12,7 @@ SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa + SUBDIR += bioparser SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 diff --git a/biology/bioparser/Makefile b/biology/bioparser/Makefile new file mode 100644 index 000000000000..ef912cc50882 --- /dev/null +++ b/biology/bioparser/Makefile @@ -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> diff --git a/biology/bioparser/distinfo b/biology/bioparser/distinfo new file mode 100644 index 000000000000..41fa93824ccc --- /dev/null +++ b/biology/bioparser/distinfo @@ -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 diff --git a/biology/bioparser/pkg-descr b/biology/bioparser/pkg-descr new file mode 100644 index 000000000000..0f798302ad87 --- /dev/null +++ b/biology/bioparser/pkg-descr @@ -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 |