svn commit: r562033 - in head/biology: . bioparser

[Yuri Victorovich]

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 at 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