biology/sra-tools: Update to 3.1.1

Numerous fixes and enhancements since 3.0.6
Changes: https://github.com/ncbi/sra-tools/commits/master/

All previous patches upstreamed
Rewrote DESCR to be more introductory

biology/sra-tools/DESCR

@@ -1,16 +1,7 @@
-SRA tools is a toolkit for using data in the INSDC Sequence Read
-Archives.  SRAs operated by the International Nucleotide Sequence
-Database Collaboration house sequence reads and alignments generated
-by "next-gen" sequencers.  SRA tools allows conversion of .sra
-files, which INSDC SRAs maintain, from/to other formats that the
-'next-gen' sequencers generate including:
-
-* csfasta/csqual (ABI SOLiD)
-* fastq (and fasta for writing)
-* hdf5 (PacBio, reading only)
-* qseq (older Illumina)
-* sam (writing only) / bam (reading only)
-* sff
-
-The toolkit uses the NCBI-VDB back-end enabling seamless access to
-remote SRA data and local SRA files.
+The SRA Toolkit and SDK from NCBI is a collection of tools and
+libraries for using data in the INSDC (International Nucleotide
+Sequence Database Collaboration) SRA (Sequence Read Archives).  The
+SRA house sequence reads and alignments generated by DNA/RNA
+sequencers.  The SRA Toolkit facilitates downloading sequence data,
+performing filtering and conversions on-the-fly, thus saving enormous
+amounts of time, bandwidth, and storage.

biology/sra-tools/Makefile

@@ -1,11 +1,9 @@
-# $NetBSD: Makefile,v 1.8 2024/11/14 22:18:47 wiz Exp $
+# $NetBSD: Makefile,v 1.9 2024/11/19 20:22:31 bacon Exp $
 
-DISTNAME=		sra-tools-3.0.6
-PKGREVISION=		6
+DISTNAME=		sra-tools-3.1.1
 CATEGORIES=		biology
-MASTER_SITES=		${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_TAG=		984f1493e8612cd59a269569bf8c06e25e4e604c
-GITHUB_SUBMODULES+=	outpaddling ncbi-vdb 38972fc ncbi-vdb
+MASTER_SITES=		${MASTER_SITE_GITHUB:=ncbi/}
+GITHUB_SUBMODULES+=	ncbi ncbi-vdb 3.1.1 ncbi-vdb
 
 OWNER=		[email protected]
 HOMEPAGE=	https://github.com/ncbi/sra-tools
@@ -18,17 +16,16 @@ ONLY_FOR_PLATFORM=	*-*-aarch64 *-*-x86_64
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	bash bison cmake
 
-# The config.c and file-path.posix.cpp substs follow
-# static patches.  Run "make clean patch" before updating
-# those patches so this subst does not get added to them.
+# SUBST edits may follow static patches.  Run "make clean patch" before
+# updating those patches so SUBST changes do not get added to them.
 SUBST_CLASSES+=		etcdir
 SUBST_STAGE.etcdir=	pre-configure
 SUBST_SED.etcdir+=	-e 's|"/etc/ncbi"|"${PREFIX}/etc/ncbi"|g'
 SUBST_FILES.etcdir+=	ncbi-vdb/libs/kfg/config.c
 
 SUBST_CLASSES+=		binpath
 SUBST_STAGE.binpath=	pre-configure
-SUBST_SED.binpath+=	-e 's|/usr/local/bin|${PREFIX}/bin|g'
+SUBST_SED.binpath+=	-e 's|/usr/local|${PREFIX}|g'
 SUBST_FILES.binpath+=	tools/external/driver-tool/file-path.posix.cpp
 
 SUBST_CLASSES+=		submoddir
@@ -38,15 +35,13 @@ SUBST_FILES.submoddir+=	CMakeLists.txt
 
 REPLACE_BASH=	*/*.sh */*/*.sh */*/*/*.sh */*/*/*/*.sh
 
-USE_CMAKE=	yes
-CMAKE_CONFIGURE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
-CMAKE_CONFIGURE_ARGS+=	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
+CMAKE_CONFIGURE_ARGS+=		-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
+CMAKE_CONFIGURE_ARGS+=		-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 BUILDLINK_TRANSFORM.NetBSD+=	rm:-ldl	# ncbi-vdb/CMakeLists.posix.txt
 
-EXAMPLESDIR=	${PREFIX}/share/examples/sra-tools
-
 .include "../../mk/bsd.prefs.mk"
 
+# macOS does not support @rpath
 .if ${OPSYS} == Darwin
 SUBST_CLASSES+=		srarpath
 SUBST_STAGE.srarpath=	post-configure
@@ -58,26 +53,15 @@ pre-configure:
 .if ${OPSYS} == NetBSD
 	# Incorrect gcc/x86_64/byteswap.h found before correct bsd/byteswap.h
 	# Adding #ifndef __NetBSD__ to gcc/x86_64/byteswap.h doesn't work
+	# Still needed as of sra-tools 3.1.1
 	${RM} -f ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64/byteswap.h
 .endif
 	cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
-.if ${OPSYS} == Darwin
-	# Unsure how to prevent cmake from emitting @rpath in the first place
-	# No instances of @rpath or -install_name in any files before cmake
-	for f in ${WRKSRC}/ncbi-vdb/build/libs/ncbi-vdb/CMakeFiles/*/link.txt; do \
-		${SED} -e 's|@rpath|${PREFIX}/lib|g' $${f} > $${f}.tmp && ${MV} -f $${f}.tmp $${f}; \
-	done
-.endif
 	cd ${WRKSRC}/ncbi-vdb/build && ${MAKE}
 
 post-install:
 	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION_NOREV}
-	${MV} ${DESTDIR}${PREFIX}/share/examples ${DESTDIR}${PREFIX}/share/examples-sratools
-	${MKDIR} ${DESTDIR}${EXAMPLESDIR}
-	${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}
-	${RMDIR} ${DESTDIR}${PREFIX}/share/examples-sratools
-	${MV} ${DESTDIR}${PREFIX}/share/examples-python ${DESTDIR}${EXAMPLESDIR}/python
-	# FIXME: Can we prevent build from detecting java?
+	${STRIP} ${DESTDIR}${PREFIX}/lib/*.${PKGVERSION_NOREV}
 	${RM} -rf ${DESTDIR}${PREFIX}/jar
 	${RM} -rf ${DESTDIR}${PREFIX}/share/examples-java
 	${RM} -rf ${DESTDIR}${PREFIX}/share/javadoc

biology/sra-tools/PLIST

@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2023/08/29 00:00:24 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2024/11/19 20:22:32 bacon Exp $
 bin/abi-dump
 bin/abi-dump.3
 bin/abi-dump.${PKGVERSION}

biology/sra-tools/distinfo

@@ -1,12 +1,14 @@
-$NetBSD: distinfo,v 1.1 2023/08/29 00:00:24 bacon Exp $
+$NetBSD: distinfo,v 1.2 2024/11/19 20:22:32 bacon Exp $
 
-BLAKE2s (outpaddling-ncbi-vdb-38972fc.tar.gz) = 600ac8ff4f2fbea9d2f06edc0277087e1559636226756eae415826dfbdb1fb5a
-SHA512 (outpaddling-ncbi-vdb-38972fc.tar.gz) = 0cda01bf2faf59aa16c4a402bcc132d4a2fc948240f6e13b2f1d3d93c4f900a837ebf8c24ee8089e88ed4de90a8ab441a4176f8193052fd7b538e27384bcb118
-Size (outpaddling-ncbi-vdb-38972fc.tar.gz) = 18978410 bytes
-BLAKE2s (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 2a13546011d4ea0a000a7e1e5fdfdf1d915b6adbac8fd818967ebf4c1670dba5
-SHA512 (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 9b1e671c92ba1006392160258c5b6fba85ba7dba59a23e9ed8b534ca31b46ed9e6cf2c92ea69dc2897f5a4aa9da31f5c8981cebb442236d11bcef76b854dbec9
-Size (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 44961381 bytes
+BLAKE2s (ncbi-ncbi-vdb-3.1.1.tar.gz) = 60e10ac43b3bfbeac580fa1680ba86291b7f2656c950e6f13d0f2021a6894029
+SHA512 (ncbi-ncbi-vdb-3.1.1.tar.gz) = ccfeb38abf8eb80d54394b4a32d851e78408d9019d1ca4b53c71681e2e9ffec904d222b2d0d32fc98fe527f66c84764ae73a8d63dada7f3b5a33c51dc3f84462
+Size (ncbi-ncbi-vdb-3.1.1.tar.gz) = 19055901 bytes
+BLAKE2s (sra-tools-3.1.1.tar.gz) = de0665b9ec114fad64b052eda29e521612ea6dddaf5555a6ed32078222834553
+SHA512 (sra-tools-3.1.1.tar.gz) = df8ae5fca3761712306db6a98074d1b1e1a02a78c09c861852a16a9bc576fc39dd6e5afe0f1572e4901786fd3a757675fe0af7e79bb85d9eac021e69e88c48f1
+Size (sra-tools-3.1.1.tar.gz) = 45754110 bytes
 SHA1 (patch-build_env.cmake) = 14add56e66e5578fd0d51ce55329285e0981ac4e
 SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
 SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
+SHA1 (patch-ngs_ngs-python_examples_CMakeLists.txt) = a8a01d17a27c060c08311ab8571ae10af265781d
+SHA1 (patch-ngs_ngs-sdk_examples_CMakeLists.txt) = 6a4b09afe4b919eeb9bd144635695437e5a3b57f
 SHA1 (patch-tools_external_driver-tool_sratools.cpp) = c490d83f03471e6e8e34b8e88534469ed45b2886

biology/sra-tools/patches/patch-build_env.cmake

@@ -1,4 +1,4 @@
-$NetBSD: patch-build_env.cmake,v 1.1 2023/08/29 00:00:25 bacon Exp $
+$NetBSD: patch-build_env.cmake,v 1.2 2024/11/19 20:22:32 bacon Exp $
 
 # static standard libs are not standard nor easy to install on Alma Linux
 

biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c

@@ -1,4 +1,4 @@
-$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.1 2023/08/29 00:00:25 bacon Exp $
+$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.2 2024/11/19 20:22:32 bacon Exp $
 
 # Add NetBSD pthread_main_np() stand-in
 

biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt

@@ -1,4 +1,4 @@
-$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.1 2023/08/29 00:00:25 bacon Exp $
+$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.2 2024/11/19 20:22:32 bacon Exp $
 
 # Disable java
 

biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt

@@ -0,0 +1,15 @@
+$NetBSD: patch-ngs_ngs-python_examples_CMakeLists.txt,v 1.1 2024/11/19 20:22:32 bacon Exp $
+
+# Canonicalize python examples dir
+
+--- ngs/ngs-python/examples/CMakeLists.txt.orig	2024-11-18 12:08:54.646596198 +0000
++++ ngs/ngs-python/examples/CMakeLists.txt
+@@ -54,7 +54,7 @@ if( Python3_EXECUTABLE )
+             RunAndDiff( RefTest "SRR1121656" )
+         endif()
+
+-        set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples-python )
++        set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools/python )
+
+         install(FILES ${SOURCES} expected.txt
+             DESTINATION ${INSTALL_DEST} )

biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt

@@ -0,0 +1,24 @@
+$NetBSD: patch-ngs_ngs-sdk_examples_CMakeLists.txt,v 1.1 2024/11/19 20:22:32 bacon Exp $
+
+# Canonicalize examples dir
+
+--- ngs/ngs-sdk/examples/CMakeLists.txt.orig	2024-11-18 12:10:46.495627136 +0000
++++ ngs/ngs-sdk/examples/CMakeLists.txt
+@@ -62,14 +62,14 @@ if ( SINGLE_CONFIG )
+     install(
+         FILES FragTest.cpp AlignTest.cpp AlignSliceTest.cpp PileupTest.cpp RefTest.cpp DumpReferenceFASTA.cpp
+               expected.txt
+-        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+     )
+     install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Makefile.install
+-        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+         RENAME Makefile
+     )
+     install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.install
+-        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+         RENAME README.txt
+     )
+ endif()

biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp

@@ -1,4 +1,4 @@
-$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.1 2023/08/29 00:00:25 bacon Exp $
+$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.2 2024/11/19 20:22:32 bacon Exp $
 
 # Add NetBSD pthread_main_np() stand-in