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biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools

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This reverts commit 1cb8897f61.

sra-tools needs to be updated first.

Reported by:	Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@
This commit is contained in:
Yuri Victorovich 2022-07-06 18:32:07 -07:00
parent 627f59813f
commit d3e9586369
8 changed files with 207 additions and 1 deletions
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1
MOVED
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@ -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sysutils/pesign||2022-07-01|Has expired: Unmaintaned since 2016, very much out of date, does not build with GCC 11 (PR #263544)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

1
biology/Makefile
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@ -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

43
biology/ngs-sdk/Makefile Normal file
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@ -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>

3
biology/ngs-sdk/distinfo Normal file
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@ -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

11
biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install Normal file
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@ -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))

37
biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl Normal file
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@ -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';

12
biology/ngs-sdk/pkg-descr Normal file
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@ -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

100
biology/ngs-sdk/pkg-plist Normal file
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@ -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