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CVS commit: pkgsrc/biology/sra-tools
Module Name: pkgsrc
Committed By: bacon
Date: Tue Aug 29 00:00:25 UTC 2023
Added Files:
pkgsrc/biology/sra-tools: DESCR Makefile PLIST distinfo
pkgsrc/biology/sra-tools/patches: patch-build_env.cmake
patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
patch-ngs_ngs-java_CMakeLists.txt
patch-tools_external_driver-tool_sratools.cpp
Log Message:
biology/sra-tools: NCBI's toolkit for SRA
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.
To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/sra-tools/DESCR \
pkgsrc/biology/sra-tools/Makefile pkgsrc/biology/sra-tools/PLIST \
pkgsrc/biology/sra-tools/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/sra-tools/patches/patch-build_env.cmake \
pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c \
pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt \
pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Added files:
Index: pkgsrc/biology/sra-tools/DESCR
diff -u /dev/null pkgsrc/biology/sra-tools/DESCR:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/DESCR Tue Aug 29 00:00:24 2023
@@ -0,0 +1,16 @@
+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.
Index: pkgsrc/biology/sra-tools/Makefile
diff -u /dev/null pkgsrc/biology/sra-tools/Makefile:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/Makefile Tue Aug 29 00:00:24 2023
@@ -0,0 +1,93 @@
+# $NetBSD: Makefile,v 1.1 2023/08/29 00:00:24 bacon Exp $
+
+DISTNAME= sra-tools-3.0.6
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_TAG= 984f1493e8612cd59a269569bf8c06e25e4e604c
+GITHUB_SUBMODULES+= outpaddling ncbi-vdb 38972fc ncbi-vdb
+
+OWNER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://github.com/ncbi/sra-tools
+COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives
+LICENSE= public-domain AND gnu-lgpl-v2.1
+
+# Upstream only supports specific platforms
+ONLY_FOR_PLATFORM= *-*-aarch64 *-*-x86_64
+
+USE_LANGUAGES= c c++
+USE_TOOLS+= bash bison cmake
+
+# The config.c and file-path.posix.cpp substs follow
+# static patches. Run "make clean patch" before updating
+# those patches so this subst does not get added to them.
+SUBST_CLASSES+= etcdir
+SUBST_STAGE.etcdir= pre-configure
+SUBST_SED.etcdir+= -e 's|"/etc/ncbi"|"${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|${PREFIX}/bin|g'
+SUBST_FILES.binpath+= tools/external/driver-tool/file-path.posix.cpp
+
+SUBST_CLASSES+= submoddir
+SUBST_STAGE.submoddir= pre-configure
+SUBST_SED.submoddir+= -e 's|/../ncbi-vdb|/ncbi-vdb|g'
+SUBST_FILES.submoddir+= CMakeLists.txt
+
+REPLACE_BASH= */*.sh */*/*.sh */*/*/*.sh */*/*/*/*.sh
+
+USE_CMAKE= yes
+CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
+CMAKE_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"
+
+.if ${OPSYS} == Darwin
+SUBST_CLASSES+= srarpath
+SUBST_STAGE.srarpath= post-configure
+SUBST_SED.srarpath+= -e 's|@rpath|${PREFIX}/lib|g'
+SUBST_FILES.srarpath+= cmake-pkgsrc-build/ngs/ngs-sdk/CMakeFiles/*/link.txt
+.endif
+
+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
+ ${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?
+ ${RM} -rf ${DESTDIR}${PREFIX}/jar
+ ${RM} -rf ${DESTDIR}${PREFIX}/share/examples-java
+ ${RM} -rf ${DESTDIR}${PREFIX}/share/javadoc
+
+.if ${OPSYS} != Linux && defined(OPSYS_HAS_KQUEUE)
+.include "../../devel/libepoll-shim/buildlink3.mk"
+.endif
+
+.include "../../mk/pthread.buildlink3.mk"
+.include "../../devel/cmake/build.mk"
+.include "../../textproc/libxml2/buildlink3.mk"
+.include "../../devel/hdf5/buildlink3.mk"
+.include "../../archivers/zstd/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/sra-tools/PLIST
diff -u /dev/null pkgsrc/biology/sra-tools/PLIST:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/PLIST Tue Aug 29 00:00:24 2023
@@ -0,0 +1,215 @@
+@comment $NetBSD: PLIST,v 1.1 2023/08/29 00:00:24 bacon Exp $
+bin/abi-dump
+bin/abi-dump.3
+bin/abi-dump.${PKGVERSION}
+bin/align-info
+bin/align-info.3
+bin/align-info.${PKGVERSION}
+bin/cache-mgr
+bin/cache-mgr.3
+bin/cache-mgr.${PKGVERSION}
+bin/check-corrupt
+bin/check-corrupt.3
+bin/check-corrupt.${PKGVERSION}
+bin/fasterq-dump
+bin/fasterq-dump-orig.${PKGVERSION}
+bin/fasterq-dump.3
+bin/fasterq-dump.${PKGVERSION}
+bin/fastq-dump
+bin/fastq-dump-orig.${PKGVERSION}
+bin/fastq-dump.3
+bin/fastq-dump.${PKGVERSION}
+bin/illumina-dump
+bin/illumina-dump.3
+bin/illumina-dump.${PKGVERSION}
+bin/kdbmeta
+bin/kdbmeta.3
+bin/kdbmeta.${PKGVERSION}
+bin/ngs-pileup
+bin/ngs-pileup.3
+bin/ngs-pileup.${PKGVERSION}
+bin/prefetch
+bin/prefetch-orig.${PKGVERSION}
+bin/prefetch.3
+bin/prefetch.${PKGVERSION}
+bin/rcexplain
+bin/rcexplain.3
+bin/rcexplain.${PKGVERSION}
+bin/ref-variation
+bin/ref-variation.3
+bin/ref-variation.${PKGVERSION}
+bin/sam-dump
+bin/sam-dump-orig.${PKGVERSION}
+bin/sam-dump.3
+bin/sam-dump.${PKGVERSION}
+bin/sff-dump
+bin/sff-dump.3
+bin/sff-dump.${PKGVERSION}
+bin/sra-info
+bin/sra-info.3
+bin/sra-info.${PKGVERSION}
+bin/sra-pileup
+bin/sra-pileup-orig.${PKGVERSION}
+bin/sra-pileup.3
+bin/sra-pileup.${PKGVERSION}
+bin/sra-search
+bin/sra-search.3
+bin/sra-search.${PKGVERSION}
+bin/sra-stat
+bin/sra-stat.3
+bin/sra-stat.${PKGVERSION}
+bin/srapath
+bin/srapath-orig.${PKGVERSION}
+bin/srapath.3
+bin/srapath.${PKGVERSION}
+bin/sratools
+bin/sratools.3
+bin/sratools.${PKGVERSION}
+bin/test-sra
+bin/test-sra.3
+bin/test-sra.${PKGVERSION}
+bin/var-expand
+bin/var-expand.3
+bin/var-expand.${PKGVERSION}
+bin/vdb-config
+bin/vdb-config.3
+bin/vdb-config.${PKGVERSION}
+bin/vdb-decrypt
+bin/vdb-decrypt.3
+bin/vdb-decrypt.${PKGVERSION}
+bin/vdb-dump
+bin/vdb-dump-orig.${PKGVERSION}
+bin/vdb-dump.3
+bin/vdb-dump.${PKGVERSION}
+bin/vdb-encrypt
+bin/vdb-encrypt.3
+bin/vdb-encrypt.${PKGVERSION}
+bin/vdb-validate
+bin/vdb-validate.3
+bin/vdb-validate.${PKGVERSION}
+include/ncbi-vdb/NGS.hpp
+include/ngs/Alignment.hpp
+include/ngs/AlignmentIterator.hpp
+include/ngs/ErrorMsg.hpp
+include/ngs/Fragment.hpp
+include/ngs/FragmentIterator.hpp
+include/ngs/Package.hpp
+include/ngs/Pileup.hpp
+include/ngs/PileupEvent.hpp
+include/ngs/PileupEventIterator.hpp
+include/ngs/PileupIterator.hpp
+include/ngs/Read.hpp
+include/ngs/ReadCollection.hpp
+include/ngs/ReadGroup.hpp
+include/ngs/ReadGroupIterator.hpp
+include/ngs/ReadIterator.hpp
+include/ngs/Reference.hpp
+include/ngs/ReferenceIterator.hpp
+include/ngs/ReferenceSequence.hpp
+include/ngs/Statistics.hpp
+include/ngs/StringRef.hpp
+include/ngs/adapter/AlignmentItf.hpp
+include/ngs/adapter/ErrorMsg.hpp
+include/ngs/adapter/FragmentItf.hpp
+include/ngs/adapter/PileupEventItf.hpp
+include/ngs/adapter/PileupItf.hpp
+include/ngs/adapter/ReadCollectionItf.hpp
+include/ngs/adapter/ReadGroupItf.hpp
+include/ngs/adapter/ReadItf.hpp
+include/ngs/adapter/Refcount.hpp
+include/ngs/adapter/ReferenceItf.hpp
+include/ngs/adapter/ReferenceSequenceItf.hpp
+include/ngs/adapter/StatisticsItf.hpp
+include/ngs/adapter/StringItf.hpp
+include/ngs/adapter/defs.h
+include/ngs/inl/Alignment.hpp
+include/ngs/inl/AlignmentIterator.hpp
+include/ngs/inl/Fragment.hpp
+include/ngs/inl/FragmentIterator.hpp
+include/ngs/inl/Package.hpp
+include/ngs/inl/Pileup.hpp
+include/ngs/inl/PileupEvent.hpp
+include/ngs/inl/PileupEventIterator.hpp
+include/ngs/inl/PileupIterator.hpp
+include/ngs/inl/Read.hpp
+include/ngs/inl/ReadCollection.hpp
+include/ngs/inl/ReadGroup.hpp
+include/ngs/inl/ReadGroupIterator.hpp
+include/ngs/inl/ReadIterator.hpp
+include/ngs/inl/Reference.hpp
+include/ngs/inl/ReferenceIterator.hpp
+include/ngs/inl/ReferenceSequence.hpp
+include/ngs/inl/Statistics.hpp
+include/ngs/inl/StringRef.hpp
+include/ngs/itf/AlignmentItf.h
+include/ngs/itf/AlignmentItf.hpp
+include/ngs/itf/ErrBlock.h
+include/ngs/itf/ErrBlock.hpp
+include/ngs/itf/ErrorMsg.hpp
+include/ngs/itf/FragmentItf.h
+include/ngs/itf/FragmentItf.hpp
+include/ngs/itf/PackageItf.hpp
+include/ngs/itf/PileupEventItf.h
+include/ngs/itf/PileupEventItf.hpp
+include/ngs/itf/PileupItf.h
+include/ngs/itf/PileupItf.hpp
+include/ngs/itf/ReadCollectionItf.h
+include/ngs/itf/ReadCollectionItf.hpp
+include/ngs/itf/ReadGroupItf.h
+include/ngs/itf/ReadGroupItf.hpp
+include/ngs/itf/ReadItf.h
+include/ngs/itf/ReadItf.hpp
+include/ngs/itf/Refcount.h
+include/ngs/itf/Refcount.hpp
+include/ngs/itf/ReferenceItf.h
+include/ngs/itf/ReferenceItf.hpp
+include/ngs/itf/ReferenceSequenceItf.h
+include/ngs/itf/ReferenceSequenceItf.hpp
+include/ngs/itf/StatisticsItf.h
+include/ngs/itf/StatisticsItf.hpp
+include/ngs/itf/StringItf.h
+include/ngs/itf/StringItf.hpp
+include/ngs/itf/VTable.h
+include/ngs/itf/VTable.hpp
+include/ngs/itf/defs.h
+include/ngs/unix/arm64/atomic32.h
+include/ngs/unix/fat86/atomic32.h
+include/ngs/unix/i386/atomic32.h
+include/ngs/unix/x86_64/atomic32.h
+include/ngs/win/atomic32.h
+include/ngs/win/stdbool.h
+lib/libncbi-ngs-c++-static.a
+lib/libncbi-ngs-c++.a
+lib/libncbi-ngs-c++.a.3
+lib/libncbi-ngs-c++.a.${PKGVERSION}
+lib/libncbi-ngs-static.a
+lib/libncbi-ngs.a
+lib/libncbi-ngs.a.3
+lib/libncbi-ngs.a.${PKGVERSION}
+lib/libncbi-ngs.so
+lib/libncbi-ngs.so.3
+lib/libncbi-ngs.so.${PKGVERSION}
+lib/libngs-c++-static.a
+lib/libngs-c++.a
+lib/libngs-c++.a.3
+lib/libngs-c++.a.${PKGVERSION}
+lib/libngs-c++.so
+lib/libngs-c++.so.3
+lib/libngs-c++.so.${PKGVERSION}
+share/examples/sra-tools/AlignSliceTest.cpp
+share/examples/sra-tools/AlignTest.cpp
+share/examples/sra-tools/DumpReferenceFASTA.cpp
+share/examples/sra-tools/FragTest.cpp
+share/examples/sra-tools/Makefile
+share/examples/sra-tools/PileupTest.cpp
+share/examples/sra-tools/README.txt
+share/examples/sra-tools/RefTest.cpp
+share/examples/sra-tools/expected.txt
+share/examples/sra-tools/python/AlignSliceTest.py
+share/examples/sra-tools/python/AlignTest.py
+share/examples/sra-tools/python/FragTest.py
+share/examples/sra-tools/python/Makefile
+share/examples/sra-tools/python/PileupTest.py
+share/examples/sra-tools/python/README.txt
+share/examples/sra-tools/python/RefTest.py
+share/examples/sra-tools/python/expected.txt
Index: pkgsrc/biology/sra-tools/distinfo
diff -u /dev/null pkgsrc/biology/sra-tools/distinfo:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/distinfo Tue Aug 29 00:00:24 2023
@@ -0,0 +1,12 @@
+$NetBSD: distinfo,v 1.1 2023/08/29 00:00:24 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
+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-tools_external_driver-tool_sratools.cpp) = c490d83f03471e6e8e34b8e88534469ed45b2886
Index: pkgsrc/biology/sra-tools/patches/patch-build_env.cmake
diff -u /dev/null pkgsrc/biology/sra-tools/patches/patch-build_env.cmake:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/patches/patch-build_env.cmake Tue Aug 29 00:00:25 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-build_env.cmake,v 1.1 2023/08/29 00:00:25 bacon Exp $
+
+# static standard libs are not standard nor easy to install on Alma Linux
+
+--- build/env.cmake.orig 2023-08-13 18:06:02.445968665 +0000
++++ build/env.cmake
+@@ -555,7 +555,7 @@ endfunction()
+ function(MakeLinksExe target install_via_driver)
+
+ if ( "GNU" STREQUAL "${CMAKE_C_COMPILER_ID}" )
+- target_link_options( ${target} PRIVATE -static-libgcc -static-libstdc++ )
++ target_link_options( ${target} PRIVATE )
+ endif()
+
+ # creates dependency loops
Index: pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
diff -u /dev/null pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c Tue Aug 29 00:00:25 2023
@@ -0,0 +1,30 @@
+$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.1 2023/08/29 00:00:25 bacon Exp $
+
+# Add NetBSD pthread_main_np() stand-in
+
+--- ncbi-vdb/libs/kproc/bsd/sysmgr.c.orig 2023-08-15 12:41:59.000000000 +0000
++++ ncbi-vdb/libs/kproc/bsd/sysmgr.c
+@@ -30,6 +30,23 @@
+ #include <pthread.h>
+ #include <unistd.h>
+
++/*
++ * NetBSD lacks non-POSIX POSIX threads functions (pthread_np)
++ */
++
++#ifdef __NetBSD__
++
++// This should be initialized to pthread_self() at the start of main()
++// If the thread ID of this thread is the same, then this is the main thread
++pthread_t _ncbi_thr_main;
++
++int pthread_main_np(void)
++
++{
++ return pthread_equal(pthread_self(), _ncbi_thr_main);
++}
++#endif
++
+ /* OnMainThread
+ * returns true if running on main thread
+ */
Index: pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
diff -u /dev/null pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt Tue Aug 29 00:00:25 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.1 2023/08/29 00:00:25 bacon Exp $
+
+# Disable java
+
+--- ngs/ngs-java/CMakeLists.txt.orig 2023-08-13 21:46:05.343038455 +0000
++++ ngs/ngs-java/CMakeLists.txt
+@@ -99,7 +99,7 @@ if ( Java_FOUND )
+ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java
+ )
+
+- find_package(JNI)
++ # find_package(JNI)
+
+ if ( JNI_FOUND )
+ add_jar( ngs-java
Index: pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
diff -u /dev/null pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp:1.1
--- /dev/null Tue Aug 29 00:00:25 2023
+++ pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp Tue Aug 29 00:00:25 2023
@@ -0,0 +1,27 @@
+$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.1 2023/08/29 00:00:25 bacon Exp $
+
+# Add NetBSD pthread_main_np() stand-in
+
+--- tools/external/driver-tool/sratools.cpp.orig 2023-08-15 12:51:29.845642918 +0000
++++ tools/external/driver-tool/sratools.cpp
+@@ -578,11 +578,20 @@ static int main(CommandLine const &argv)
+
+ } // namespace sratools
+
++#ifdef __NetBSD__
++// Defined in sysmgr.c
++extern pthread_t _ncbi_thr_main;
++#endif
++
+ // BSD is defined when compiling on Mac
+ // Use the MAC case below, not this one
+ #if BSD && !MAC
+ int main(int argc, char *argv[], char *envp[])
+ {
++#ifdef __NetBSD__
++ _ncbi_thr_main = pthread_self();
++#endif
++
+ auto const invocation = CommandLine(argc, argv, envp, nullptr);
+ return sratools::main(invocation);
+ }
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