svn commit: r472158 - in head/biology: . ngs-sdk ngs-sdk/files
Yuri Victorovich
yuri at FreeBSD.org
Sun Jun 10 23:58:10 UTC 2018
Author: yuri
Date: Sun Jun 10 23:58:07 2018
New Revision: 472158
URL: https://svnweb.freebsd.org/changeset/ports/472158
Log:
New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Sequence Read Archives
Added:
head/biology/ngs-sdk/
head/biology/ngs-sdk/Makefile (contents, props changed)
head/biology/ngs-sdk/distinfo (contents, props changed)
head/biology/ngs-sdk/files/
head/biology/ngs-sdk/files/patch-Makefile (contents, props changed)
head/biology/ngs-sdk/files/patch-configure (contents, props changed)
head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl (contents, props changed)
head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl (contents, props changed)
head/biology/ngs-sdk/pkg-descr (contents, props changed)
head/biology/ngs-sdk/pkg-plist (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Sun Jun 10 20:28:15 2018 (r472157)
+++ head/biology/Makefile Sun Jun 10 23:58:07 2018 (r472158)
@@ -64,6 +64,7 @@
SUBDIR += muscle
SUBDIR += ncbi-blast+
SUBDIR += ncbi-toolkit
+ SUBDIR += ngs-sdk
SUBDIR += njplot
SUBDIR += p5-AcePerl
SUBDIR += p5-Bio-ASN1-EntrezGene
Added: head/biology/ngs-sdk/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/Makefile Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,36 @@
+# $FreeBSD$
+
+PORTNAME= ngs
+DISTVERSION= 2.9.0
+CATEGORIES= biology
+PKGNAMESUFFIX= -sdk
+
+MAINTAINER= yuri at FreeBSD.org
+COMMENT= Tools and libraries for using data in the INSDC Sequence Read Archives
+
+LICENSE= PD
+LICENSE_FILE= ${WRKSRC}/LICENSE
+
+USES= gmake perl5
+GNU_CONFIGURE= yes
+USE_GITHUB= yes
+GH_ACCOUNT= ncbi
+ALL_TARGET= default
+USE_LDCONFIG= yes
+
+CFLAGS+= -I${WRKSRC}/ngs-sdk/ngs/unix/${ARCH}/
+
+post-patch:
+ @cd ${WRKSRC}/ngs-sdk/ngs/unix && ${LN} -s x86_64 amd64
+
+do-install:
+ cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}/${PREFIX}/include
+ ${INSTALL_PROGRAM} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/libngs-sdk.so.${DISTVERSION} ${STAGEDIR}${PREFIX}/lib/
+ cd ${STAGEDIR}${PREFIX}/lib/ && \
+ ${LN} -s libngs-sdk.so.${DISTVERSION} libngs-sdk.so.${DISTVERSION:R:R} && \
+ ${LN} -s libngs-sdk.so.${DISTVERSION:R:R} libngs-sdk.so
+.for l in libngs-c++.a libngs-adapt-c++.a
+ ${INSTALL_LIB} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/${l}.${PORTVERSION} ${STAGEDIR}${PREFIX}/lib/${l}
+.endfor
+
+.include <bsd.port.mk>
Added: head/biology/ngs-sdk/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/distinfo Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1528660489
+SHA256 (ncbi-ngs-2.9.0_GH0.tar.gz) = 7e4f9e4490309b6fb33ec9370e5202ad446b10b75c323ba8226c29ca364a0857
+SIZE (ncbi-ngs-2.9.0_GH0.tar.gz) = 1091488
Added: head/biology/ngs-sdk/files/patch-Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/files/patch-Makefile Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,13 @@
+--- Makefile.orig 2018-06-10 19:59:04 UTC
++++ Makefile
+@@ -27,9 +27,7 @@ default: subdirs
+
+ # the sub-directories
+ SUBDIRS = \
+- ngs-sdk \
+- ngs-java \
+- ngs-python \
++ ngs-sdk
+
+ SUBDIRS_CLN = \
+ $(addsuffix _cln,$(SUBDIRS))
Added: head/biology/ngs-sdk/files/patch-configure
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/files/patch-configure Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,11 @@
+--- configure.orig 2018-06-10 19:58:29 UTC
++++ configure
+@@ -41,7 +41,7 @@ if [ "$FILENAME" != configure -a ! -s co
+ echo configure: error: configure should be run as ./configure
+ else
+ cd $CURDIR
+- for D in ngs-sdk ngs-java ngs-python
++ for D in ngs-sdk
+ do
+ if [ -d $D ]
+ then echo "CONFIGURING $D"
Added: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,13 @@
+--- ngs-sdk/setup/install.perl.orig 2018-06-10 20:03:25 UTC
++++ ngs-sdk/setup/install.perl
+@@ -1283,8 +1283,8 @@ sub prepare {
+ ' $_{INST_JARDIR } = "$_{PREFIX}/jar"; ' .
+ ' $_{INST_SHAREDIR} = "$_{PREFIX}/share"; ' .
+ ' $_{INCDIR } = "$Bin/../include"; ' .
+- ' $_{LIBDIR64 } = "$Bin/../lib64"; ' .
+- ' $_{LIBDIR32 } = "$Bin/../lib32"; ';
++ ' $_{LIBDIR64 } = "$Bin/../lib"; ' .
++ ' $_{LIBDIR32 } = "$Bin/../lib"; ';
+ if ($HAVE{TWO_LIBS}) {
+ $code .=
+ '$_{INST_NGSLIBDIR} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";"
Added: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,72 @@
+--- ngs-sdk/setup/konfigure.perl.orig 2018-02-23 22:53:52 UTC
++++ ngs-sdk/setup/konfigure.perl
+@@ -202,7 +202,7 @@ print "checking system type... " unless
+ my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
+ println $OSTYPE unless ($AUTORUN);
+
+-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'FreeBSD') {
+ println "configure: error: unsupported system '$OSTYPE'";
+ exit 1;
+ }
+@@ -215,6 +215,10 @@ if ($OS eq 'linux') {
+ println $OS_DISTRIBUTOR unless ($AUTORUN);
+ }
+
++if ($MARCH eq 'amd64') {
++ $MARCH = 'x86_64';
++}
++
+ print "checking machine architecture... " unless ($AUTORUN);
+ println $MARCH unless ($AUTORUN);
+ unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
+@@ -326,6 +330,16 @@ if ($OSTYPE =~ /linux/i) {
+ $EXEX = '';
+ $OSINC = 'unix';
+ $TOOLS = 'gcc' unless ($TOOLS);
++} elsif ($OSTYPE =~ /freebsd/i) {
++ $BITS = '';
++ $LPFX = 'lib';
++ $OBJX = 'o';
++ $LOBX = 'pic.o';
++ $LIBX = 'a';
++ $SHLX = 'so';
++ $EXEX = '';
++ $OSINC = 'unix';
++ $TOOLS = 'clang' unless ($TOOLS);
+ } elsif ($OSTYPE =~ /darwin/i) {
+ $LPFX = 'lib';
+ $OBJX = 'o';
+@@ -371,11 +385,11 @@ if ($TOOLS =~ /gcc$/) {
+ } elsif ($TOOLS eq 'clang') {
+ $CPP = 'clang++' unless ($CPP);
+ $CC = 'clang -c';
+- my $versionMin = '-mmacosx-version-min=10.6';
++ my $versionMin = '';
+ $CP = "$CPP -c $versionMin";
+ if ($BITS ne '32_64') {
+ $ARCH_FL = '-arch i386' if ($BITS == 32);
+- $OPT = '-O3';
++ $OPT = $ENV{'CXXFLAGS'};
+ $AR = 'ar rc';
+ $LD = "clang $ARCH_FL";
+ $LP = "$CPP $versionMin $ARCH_FL";
+@@ -463,7 +477,7 @@ foreach my $href (DEPENDS()) {
+ $I = $t if (-e $t);
+ }
+ push ( @L, File::Spec->catdir($OPT{$o}, 'lib') );
+- push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
++ #push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
+ }
+ my ($i, $l) = find_lib($_, $I, @L);
+ if (defined $i || $l) {
+@@ -881,8 +895,7 @@ EndText
+ L($F, "PIC = $PIC") if ($PIC);
+ if ($PKG{LNG} eq 'C') {
+ if ($TOOLS =~ /clang/i) {
+- L($F, 'SONAME = -install_name ' .
+- '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
++ L($F, 'SONAME = -Wl,-soname=$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
+ L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
+ L($F, ' -flat_namespace -undefined suppress');
+ } else {
Added: head/biology/ngs-sdk/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/pkg-descr Sun Jun 10 23:58:07 2018 (r472158)
@@ -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
Added: head/biology/ngs-sdk/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ngs-sdk/pkg-plist Sun Jun 10 23:58:07 2018 (r472158)
@@ -0,0 +1,95 @@
+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/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/libngs-adapt-c++.a
+lib/libngs-c++.a
+lib/libngs-sdk.so
+lib/libngs-sdk.so.2
+lib/libngs-sdk.so.2.9.0
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