git: 1cb8897f610a - main - biology/ngs-sdk: Remove, ngs was moved into sra-tools

Reply: Colin Percival : "Re: git: 1cb8897f610a - main - biology/ngs-sdk: Remove, ngs was moved into sra-tools"
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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Wed, 06 Jul 2022 19:06:25 UTC
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 sysutils/pesign||2022-07-01|Has expired: Unmaintaned since 2016, very much out of date, does not build with GCC 11 (PR #263544)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