Date: Wed, 6 Jul 2022 19:06:25 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 1cb8897f610a - main - biology/ngs-sdk: Remove, ngs was moved into sra-tools Message-ID: <202207061906.266J6PP7047173@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=1cb8897f610a381ddf2802eb09acfba97b15b505 commit 1cb8897f610a381ddf2802eb09acfba97b15b505 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-07-06 19:03:11 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-07-06 19:03:11 +0000 biology/ngs-sdk: Remove, ngs was moved into sra-tools --- MOVED | 1 + biology/Makefile | 1 - biology/ngs-sdk/Makefile | 43 --------- biology/ngs-sdk/distinfo | 3 - .../ngs-sdk/files/patch-ngs-sdk_Makefile.install | 11 --- .../files/patch-ngs-sdk_setup_konfigure.perl | 37 -------- biology/ngs-sdk/pkg-descr | 12 --- biology/ngs-sdk/pkg-plist | 100 --------------------- 8 files changed, 1 insertion(+), 207 deletions(-) diff --git a/MOVED b/MOVED index 9372e586ae59..a7b5f52d4d77 100644 --- a/MOVED +++ b/MOVED @@ -17491,3 +17491,4 @@ sysutils/go-btfs||2022-07-01|Has expired: Requires go 1.15 sysutils/pesign||2022-07-01|Has expired: Unmaintaned since 2016, very much out of date, does not build with GCC 11 (PR #263544) sysutils/cfengine316||2022-07-06|Has expired: Expire one year after cfengine 3.18.0 released sysutils/cfengine-masterfiles316||2022-07-06|Has expired: Expire one year after cfengine 3.18.0 released +biology/ngs-sdk|biology/sra-tools|2022-07-06|ngs was moved into sra-tools by the upstream diff --git a/biology/Makefile b/biology/Makefile index 422c8fdd52b4..c67a064d6afa 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -101,7 +101,6 @@ SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb - SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster diff --git a/biology/ngs-sdk/Makefile b/biology/ngs-sdk/Makefile deleted file mode 100644 index 2a6e174bbf5f..000000000000 --- a/biology/ngs-sdk/Makefile +++ /dev/null @@ -1,43 +0,0 @@ -PORTNAME= ngs -DISTVERSION= 2.11.2 -CATEGORIES= biology -PKGNAMESUFFIX= -sdk - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Tools and libraries for using data in the INSDC Sequence Read Archives - -LICENSE= PD -LICENSE_FILE= ${WRKSRC}/LICENSE - -BROKEN_aarch64= fails to configure: unsupported architecture 'FreeBSD' -BROKEN_riscv64= fails to configure: unsupported architecture 'FreeBSD' -NOT_FOR_ARCHS= powerpc64 -NOT_FOR_ARCHS_REASON= os-arch.prl needs to be taught about powerpc64 - -USES= compiler:c++11-lang gmake perl5 -USE_PERL5= build -USE_LDCONFIG= yes - -USE_GITHUB= yes -GH_ACCOUNT= ncbi - -HAS_CONFIGURE= yes -CONFIGURE_ARGS= --prefix="${STAGEDIR}${PREFIX}" --build-prefix="${WRKSRC}/build" - -ALL_TARGET= ngs-sdk - -post-extract: - @cd ${WRKSRC}/ngs-sdk/ngs/unix && ${LN} -s x86_64 amd64 - -do-install: # install target from the project breaks: https://github.com/ncbi/ngs/issues/34 - # install headers - cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}${PREFIX}/include - ${RM} -r ${STAGEDIR}${PREFIX}/include/ngs/win - # install libraries - cd ${WRKSRC}/build/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/lib - # The above command installs broken-looking static libs with symlinks. - # This is intentional, see comments https://github.com/ncbi/ncbi-vdb/issues/36#issuecomment-817990790 This may change in future versions. - # strip - ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libngs-sdk.so.${DISTVERSION} - -.include <bsd.port.mk> diff --git a/biology/ngs-sdk/distinfo b/biology/ngs-sdk/distinfo deleted file mode 100644 index 922f4ad62f65..000000000000 --- a/biology/ngs-sdk/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1643246050 -SHA256 (ncbi-ngs-2.11.2_GH0.tar.gz) = 7555ab7c2f04bd81160859f6c85c65376dc7f7b891804fad9e7636a7788e39c2 -SIZE (ncbi-ngs-2.11.2_GH0.tar.gz) = 1101119 diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install deleted file mode 100644 index b9cf320d1f6d..000000000000 --- a/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install +++ /dev/null @@ -1,11 +0,0 @@ ---- ngs-sdk/Makefile.install.orig 2021-04-12 08:00:01 UTC -+++ ngs-sdk/Makefile.install -@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \ - ngs-c++.$(VERSION_LIBX) \ - ngs-adapt-c++.$(VERSION_LIBX) \ - --LIB_TARGET = $(INST_LIBDIR)$(BITS) -+LIB_TARGET = $(INST_LIBDIR) - - LIBRARIES_WITH_PREFIX = \ - $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL)) diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl deleted file mode 100644 index 5fc8fb532a2c..000000000000 --- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl +++ /dev/null @@ -1,37 +0,0 @@ ---- ngs-sdk/setup/konfigure.perl.orig 2021-08-18 16:26:23 UTC -+++ ngs-sdk/setup/konfigure.perl -@@ -225,7 +225,7 @@ if ($OS eq 'linux') { - - print "checking machine architecture... " unless ($AUTORUN); - println $MARCH unless ($AUTORUN); --unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { -+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { - println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'"; - exit 1; - } -@@ -312,6 +312,8 @@ my $BITS; - - if ($MARCH =~ /x86_64/i) { - $BITS = 64; -+} elsif ($MARCH =~ /amd64/i) { -+ $BITS = 64; - } elsif ($MARCH eq 'fat86') { - $BITS = '32_64'; - } elsif ($MARCH =~ /i?86/i) { -@@ -337,6 +339,16 @@ if ($OSTYPE =~ /linux/i) { - $OSINC = 'unix'; - $TOOLS = 'gcc' unless ($TOOLS); - $PYTHON = 'python'; -+} elsif ($OSTYPE =~ /freebsd/i) { -+ $LPFX = 'lib'; -+ $OBJX = 'o'; -+ $LOBX = 'pic.o'; -+ $LIBX = 'a'; -+ $SHLX = 'so'; -+ $EXEX = ''; -+ $OSINC = 'unix'; -+ $TOOLS = 'clang' unless ($TOOLS); -+ $PYTHON = $ENV{FREEBSD_PYTHON_CMD}; - } elsif ($OSTYPE =~ /darwin/i) { - $LPFX = 'lib'; - $OBJX = 'o'; diff --git a/biology/ngs-sdk/pkg-descr b/biology/ngs-sdk/pkg-descr deleted file mode 100644 index b52c80174755..000000000000 --- a/biology/ngs-sdk/pkg-descr +++ /dev/null @@ -1,12 +0,0 @@ -NGS is a new, domain-specific API for accessing reads, alignments and pileups -produced from Next Generation Sequencing. The API itself is independent from any -particular back-end implementation, and supports use of multiple back-ends -simultaneously. It also provides a library for building new back-end "engines". -The engine for accessing SRA data is contained within the sister repository -ncbi-vdb. - -The API is currently expressed in C++, Java and Python languages. The design -makes it possible to maintain a high degree of similarity between the code in -one language and code in another - especially between C++ and Java. - -WWW: https://github.com/ncbi/ngs diff --git a/biology/ngs-sdk/pkg-plist b/biology/ngs-sdk/pkg-plist deleted file mode 100644 index 958bceed7edc..000000000000 --- a/biology/ngs-sdk/pkg-plist +++ /dev/null @@ -1,100 +0,0 @@ -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/amd64 -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 -lib/libngs-adapt-c++-static.a -lib/libngs-adapt-c++.a -lib/libngs-adapt-c++.a.2 -lib/libngs-adapt-c++.a.2.11.2 -lib/libngs-c++-static.a -lib/libngs-c++.a -lib/libngs-c++.a.2 -lib/libngs-c++.a.2.11.2 -lib/libngs-sdk.so -lib/libngs-sdk.so.2 -lib/libngs-sdk.so.2.11.2
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