Date: Thu, 7 Jul 2022 01:34:33 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: d3e958636916 - main - biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools Message-ID: <202207070134.2671YXL4075044@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=d3e958636916e711fa0437b21b617c16f026d64e commit d3e958636916e711fa0437b21b617c16f026d64e Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-07-07 01:32:07 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-07-07 01:33:58 +0000 biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools This reverts commit 1cb8897f610a381ddf2802eb09acfba97b15b505. sra-tools needs to be updated first. Reported by: Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@ --- 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, 207 insertions(+), 1 deletion(-) diff --git a/MOVED b/MOVED index a7b5f52d4d77..9372e586ae59 100644 --- a/MOVED +++ b/MOVED @@ -17491,4 +17491,3 @@ 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expired: Requires go 1.15 sysutils/pesign||2022-07-01|Has expired: Unmaintaned since 2016, very much out of date, does not build with GCC 11 (PR #263544) sysutils/cfengine316||2022-07-06|Has expired: Expire one year after cfengine 3.18.0 released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 c67a064d6afa..422c8fdd52b4 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -101,6 +101,7 @@ 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 new file mode 100644 index 000000000000..2a6e174bbf5f --- /dev/null +++ b/biology/ngs-sdk/Makefile @@ -0,0 +1,43 @@ +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.${DISTVERSION} + +.include <bsd.port.mk> diff --git a/biology/ngs-sdk/distinfo b/biology/ngs-sdk/distinfo new file mode 100644 index 000000000000..922f4ad62f65 --- /dev/null +++ b/biology/ngs-sdk/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1643246050 +SHA256 (ncbi-ngs-2.11.2_GH0.tar.gz) = 7555ab7c2f04bd81160859f6c85c65376dc7f7b891804fad9e7636a7788e39c2 +SIZE (ncbi-ngs-2.11.2_GH0.tar.gz) = 1101119 diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install new file mode 100644 index 000000000000..b9cf320d1f6d --- /dev/null +++ b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install @@ -0,0 +1,11 @@ +--- ngs-sdk/Makefile.install.orig 2021-04-12 08:00:01 UTC ++++ ngs-sdk/Makefile.install +@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \ + ngs-c++.$(VERSION_LIBX) \ + ngs-adapt-c++.$(VERSION_LIBX) \ + +-LIB_TARGET = $(INST_LIBDIR)$(BITS) ++LIB_TARGET = $(INST_LIBDIR) + + LIBRARIES_WITH_PREFIX = \ + $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL)) diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl new file mode 100644 index 000000000000..5fc8fb532a2c --- /dev/null +++ b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl @@ -0,0 +1,37 @@ +--- ngs-sdk/setup/konfigure.perl.orig 2021-08-18 16:26:23 UTC ++++ ngs-sdk/setup/konfigure.perl +@@ -225,7 +225,7 @@ if ($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 new file mode 100644 index 000000000000..b52c80174755 --- /dev/null +++ b/biology/ngs-sdk/pkg-descr @@ -0,0 +1,12 @@ +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 new file mode 100644 index 000000000000..958bceed7edc --- /dev/null +++ b/biology/ngs-sdk/pkg-plist @@ -0,0 +1,100 @@ +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
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202207070134.2671YXL4075044>