biology/sra-tools: Update to 3.0.6

Major code and build system rework since 2.11
Now supports aarch64, unblocking rna-seq and atac-seq metaports
Changes: https://github.com/ncbi/sra-tools/commits/master

Reported by:    portscout

biology/sra-tools/Makefile

@@ -1,109 +1,67 @@
 PORTNAME=	sra-tools
-DISTVERSION=	2.11.0
-PORTREVISION=	4
-CATEGORIES=	biology
+DISTVERSION=	3.0.6
+CATEGORIES=	biology java
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
-WWW=		https://github.com/ncbi/sra-tools/wiki
+WWW=		https://github.com/ncbi/sra-tools
 
 LICENSE=		PD LGPL21+
 LICENSE_COMB=		multi
 LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 LICENSE_DISTFILES_LGPL21+ =
 
-ONLY_FOR_ARCHS=		amd64
-ONLY_FOR_ARCHS_REASON=	NCBI-VDB requires SSE2 instructions, no 32-bit support
+# Untested on other platforms, aarch64 support was recently added upstream
+ONLY_FOR_ARCHS=		aarch64 amd64
+ONLY_FOR_ARCHS_REASON=	Upstream explicitly supports specific platforms
 
-BUILD_DEPENDS=	bash:shells/bash \
-		${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
+BUILD_DEPENDS=	bash:shells/bash
 LIB_DEPENDS=	libxml2.so:textproc/libxml2 \
 		libhdf5.so:science/hdf5 \
-		libepoll-shim.so:devel/libepoll-shim
+		libepoll-shim.so:devel/libepoll-shim \
+		libzstd.so:archivers/zstd
 
-USES=		compiler:c11 gmake localbase:ldflags perl5 shebangfix
-USE_PERL5=	build
+USES=		bison cmake shebangfix
 USE_GITHUB=	yes
+USE_LDCONFIG=	${PREFIX}/lib64
+USE_JAVA=	yes
 
-SHEBANG_GLOB=	*.sh *.pl
-GH_ACCOUNT=	ncbi
-GH_TUPLE+=	ncbi:ngs:${DISTVERSION}:ngs/ngs # ported as biology/ngs-sdk
-GH_TUPLE+=	ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
-
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--with-ngs-sdk-prefix=${LOCALBASE} \
-		--with-ncbi-vdb-sources=${NCBI_VDB_WRKSRC} \
-		--with-xml2-prefix=${LOCALBASE} \
-		--with-hdf5-prefix=${LOCALBASE} \
-		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" \
-		--with-ncbi-vdb-build=${NCBI_VDB_WRKSRC}/amd64-portbld-freebsd$$(${FREEBSD_RELEASE})
-MAKE_ARGS=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
-		INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
-
-NCBI_VDB_WRKSRC=	${WRKSRC}/ncbi-vdb
-NCBI_VDB_FILESDIR=	${FILESDIR}
-FREEBSD_RELEASE=	uname -r | cut -d - -f 1
-
-CFLAGS+=	-I${WRKSRC}/interfaces/os/sun
-CXXFLAGS+=	-I${WRKSRC}/interfaces/os/sun
-
-CONFLICTS_INSTALL=	kget
+# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
+JAVA_VERSION=	17+
 
-BINARY_ALIAS=	gcc=${CC} g++=${CXX}
+OPTIONS_DEFINE=	EXAMPLES
 
-# for port developers, building with these options may fail
-OPTIONS_DEFINE=		DEBUG OPTIMIZED_CFLAGS TEST
-DEBUG_PREVENTS=		OPTIMIZED_CFLAGS
-DEBUG_CONFIGURE_WITH=	debug
-OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
-TEST_TEST_TARGET=	test
-TEST_USES=		python
-
-# ncbi-vdb build extras
-VDB_CONFIGURE_ARGS=	\
-		--with-xml2-prefix=${LOCALBASE} \
-		--with-hdf5-prefix=${LOCALBASE} \
-		--prefix=${PREFIX} \
-		--build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \
-		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
-VDB_MAKE_ARGS+=	-j 1 CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
-MAKE_ENV+=	CPATH="${LOCALBASE}/include/libepoll-shim"
-CFLAGS+=	-I${WRKSRC}/lib
-
-pre-patch:
-	@${CP} ${FILESDIR}/Makefile.bsd ${NCBI_VDB_WRKSRC}/build/
-	@${CP} ${FILESDIR}/ld.bsd.*.sh ${NCBI_VDB_WRKSRC}/build/
-	@${MKDIR} ${NCBI_VDB_WRKSRC}/interfaces/os/bsd
-	@${CP} -p ${NCBI_VDB_WRKSRC}/interfaces/os/mac/endian.h \
-		${NCBI_VDB_WRKSRC}/interfaces/os/bsd/
+SHEBANG_GLOB=	*.sh
+GH_ACCOUNT=	ncbi
+GH_TUPLE+=	ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
 
-post-patch:
-	@${GREP} -q '@@PREFIX@@' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)
-	@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c
-	@${LN} -s ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64
+WITH_DEBUG=	yes
+CMAKE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
 
-post-patch-TEST-on:
-	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile
+post-extract:
+	@${MKDIR} ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
+	@${CP} ${FILESDIR}/*.h ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
+	# cd ${WRKDIR} && ${LN} -s ${WRKSRC}/ncbi-vdb .
 
 pre-configure:
-	@${CP} ${NCBI_VDB_WRKSRC}/setup/os-arch.prl ${WRKSRC}/setup/os-arch.prl
-	# same as in biology/ncbi-vdb
-	@${CP} ${NCBI_VDB_FILESDIR}/Makefile.bsd ${WRKSRC}/build/
-	@${CP} ${NCBI_VDB_WRKSRC}/build/ld.bsd.*.sh ${WRKSRC}/build/
-	@${MKDIR} ${WRKSRC}/interfaces/override
-	@${CP} ${NCBI_VDB_WRKSRC}/interfaces/os/sun/atomic32.h ${WRKSRC}/interfaces/override
-	@${CP} ${FILESDIR}/byteswap.h ${WRKSRC}/interfaces/override
-	@cd ${WRKSRC}/ncbi-vdb && ./configure ${VDB_CONFIGURE_ARGS}
-	@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/ncbi-vdb/build/COMP
-	@cd ${WRKSRC}/ncbi-vdb && ${DO_MAKE_BUILD} ${VDB_MAKE_ARGS}
-
-post-build-TEST-on:	do-test
-
-do-install:
-	cd ${WRKSRC}/amd64-portbld-freebsd*/sra-tools/bsd/clang/*/rel/bin && \
-	    for f in `ls *.${PORTVERSION}`; do \
-		${INSTALL_PROGRAM} $${f} \
-		${STAGEDIR}${PREFIX}/bin/`basename $${f%%.${PORTVERSION}}`; \
-	done
+	# This follows a static patch.  Run "make clean patch" before
+	# updating the patch.
+	${REINPLACE_CMD} -e 's|/usr/local/etc/ncbi|${PREFIX}/etc/ncbi|g' \
+		${WRKSRC}/ncbi-vdb/libs/kfg/config.c
+	${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
+		${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
+	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
+
+post-stage:
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
+	${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools
+	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR}
+	${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools
+	${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java
+	${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python
+
+post-stage-EXAMPLES-off:
+	${RM} -r ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>

biology/sra-tools/distinfo

@@ -1,7 +1,5 @@
-TIMESTAMP = 1624382289
-SHA256 (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810
-SIZE (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 8966605
-SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc
-SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365
-SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa
-SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539
+TIMESTAMP = 1691599515
+SHA256 (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 9fecfd819ee9beaf8a1d3e4b76a5d49e747bc064525b40416e0730a168986348
+SIZE (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 44957431
+SHA256 (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 4b6f93336bf8664fdcc151d41ea0793f0b0f88cfcb7c2aa049f162a72f905223
+SIZE (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 18972238

biology/sra-tools/files/byteswap.h

@@ -1,40 +1,15 @@
-/*===========================================================================
-*
-*                            PUBLIC DOMAIN NOTICE
-*               National Center for Biotechnology Information
-*
-*  This software/database is a "United States Government Work" under the
-*  terms of the United States Copyright Act.  It was written as part of
-*  the author's official duties as a United States Government employee and
-*  thus cannot be copyrighted.  This software/database is freely available
-*  to the public for use. The National Library of Medicine and the U.S.
-*  Government have not placed any restriction on its use or reproduction.
-*
-*  Although all reasonable efforts have been taken to ensure the accuracy
-*  and reliability of the software and data, the NLM and the U.S.
-*  Government do not and cannot warrant the performance or results that
-*  may be obtained by using this software or data. The NLM and the U.S.
-*  Government disclaim all warranties, express or implied, including
-*  warranties of performance, merchantability or fitness for any particular
-*  purpose.
-*
-*  Please cite the author in any work or product based on this material.
-*
-* ===========================================================================
-*
-*/
 
-#ifndef _h_byteswap_
-#define _h_byteswap_
+#ifndef _freebsd_byteswap_h_
+#define _freebsd_byteswap_h_
 
-#include <stdint.h>
 #include <sys/endian.h>
 
-/* N.B. Sun's BSWAP seems to be macro-based,
-   meaning that (x) will be evaluated multiple times */
+#define	__BYTE_ORDER	_BYTE_ORDER
+#define	__BIG_ENDIAN	_BIG_ENDIAN
+#define	__LITTLE_ENDIAN	_LITTLE_ENDIAN
 
 #define bswap_16(x) bswap16 (x)
 #define bswap_32(x) bswap32 (x)
 #define bswap_64(x) bswap64 (x)
 
-#endif /* _h_byteswap_ */
+#endif

biology/sra-tools/files/endian.h

@@ -0,0 +1,2 @@
+
+#include <sys/endian.h>