Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 472157) +++ head/biology/Makefile (revision 472158) @@ -1,138 +1,139 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit + SUBDIR += ngs-sdk SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/ngs-sdk/Makefile =================================================================== --- head/biology/ngs-sdk/Makefile (nonexistent) +++ head/biology/ngs-sdk/Makefile (revision 472158) @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= ngs +DISTVERSION= 2.9.0 +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= ${WRKSRC}/LICENSE + +USES= gmake perl5 +GNU_CONFIGURE= yes +USE_GITHUB= yes +GH_ACCOUNT= ncbi +ALL_TARGET= default +USE_LDCONFIG= yes + +CFLAGS+= -I${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 Property changes on: head/biology/ngs-sdk/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/distinfo =================================================================== --- head/biology/ngs-sdk/distinfo (nonexistent) +++ head/biology/ngs-sdk/distinfo (revision 472158) @@ -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 Property changes on: head/biology/ngs-sdk/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/files/patch-Makefile =================================================================== --- head/biology/ngs-sdk/files/patch-Makefile (nonexistent) +++ head/biology/ngs-sdk/files/patch-Makefile (revision 472158) @@ -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)) Property changes on: head/biology/ngs-sdk/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/files/patch-configure =================================================================== --- head/biology/ngs-sdk/files/patch-configure (nonexistent) +++ head/biology/ngs-sdk/files/patch-configure (revision 472158) @@ -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" Property changes on: head/biology/ngs-sdk/files/patch-configure ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl =================================================================== --- head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl (nonexistent) +++ head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl (revision 472158) @@ -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} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";" Property changes on: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl =================================================================== --- head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl (nonexistent) +++ head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl (revision 472158) @@ -0,0 +1,72 @@ +--- ngs-sdk/setup/konfigure.perl.orig 2018-02-23 22:53:52 UTC ++++ ngs-sdk/setup/konfigure.perl +@@ -202,7 +202,7 @@ print "checking system type... " unless + my ($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 { Property changes on: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/pkg-descr =================================================================== --- head/biology/ngs-sdk/pkg-descr (nonexistent) +++ head/biology/ngs-sdk/pkg-descr (revision 472158) @@ -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 Property changes on: head/biology/ngs-sdk/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ngs-sdk/pkg-plist =================================================================== --- head/biology/ngs-sdk/pkg-plist (nonexistent) +++ head/biology/ngs-sdk/pkg-plist (revision 472158) @@ -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 Property changes on: head/biology/ngs-sdk/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property