Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 465807) +++ head/biology/Makefile (revision 465808) @@ -1,122 +1,123 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne 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 += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib 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 += 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 += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink 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 += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/bamtools/Makefile =================================================================== --- head/biology/bamtools/Makefile (nonexistent) +++ head/biology/bamtools/Makefile (revision 465808) @@ -0,0 +1,22 @@ +# $FreeBSD$ + +PORTNAME= bamtools +DISTVERSIONPREFIX= v +DISTVERSION= 2.5.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= API and toolkit for handling BAM files + +LICENSE= MIT + +LIB_DEPENDS+= libjsoncpp.so:devel/jsoncpp + +USES= cmake:outsource +USE_LDCONFIG= yes +USE_GITHUB= yes +GH_ACCOUNT= pezmaster31 + +CMAKE_ON+= BUILD_SHARED_LIBS + +.include Property changes on: head/biology/bamtools/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/bamtools/distinfo =================================================================== --- head/biology/bamtools/distinfo (nonexistent) +++ head/biology/bamtools/distinfo (revision 465808) @@ -0,0 +1,3 @@ +TIMESTAMP = 1520126058 +SHA256 (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc +SIZE (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 549750 Property changes on: head/biology/bamtools/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/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp =================================================================== --- head/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp (nonexistent) +++ head/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp (revision 465808) @@ -0,0 +1,11 @@ +--- src/api/internal/io/HostInfo_p.cpp.orig 2015-06-16 16:50:53 UTC ++++ src/api/internal/io/HostInfo_p.cpp +@@ -11,6 +11,8 @@ + using namespace BamTools; + using namespace BamTools::Internal; + ++#include ++ + // platorm-specifics + #ifdef _WIN32 + # include "api/internal/io/NetWin_p.h" Property changes on: head/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp ___________________________________________________________________ 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/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp =================================================================== --- head/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp (nonexistent) +++ head/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp (revision 465808) @@ -0,0 +1,11 @@ +--- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig 2015-06-16 16:50:53 UTC ++++ src/api/internal/io/TcpSocketEngine_unix_p.cpp +@@ -12,6 +12,8 @@ + using namespace BamTools; + using namespace BamTools::Internal; + ++#include ++ + #ifdef SUN_OS + #include + #endif Property changes on: head/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp ___________________________________________________________________ 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/bamtools/pkg-descr =================================================================== --- head/biology/bamtools/pkg-descr (nonexistent) +++ head/biology/bamtools/pkg-descr (revision 465808) @@ -0,0 +1,4 @@ +BamTools provides both a programmer's API and an end-user's toolkit for +handling BAM files. + +WWW: https://github.com/pezmaster31/bamtools Property changes on: head/biology/bamtools/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/bamtools/pkg-plist =================================================================== --- head/biology/bamtools/pkg-plist (nonexistent) +++ head/biology/bamtools/pkg-plist (revision 465808) @@ -0,0 +1,24 @@ +bin/bamtools +include/bamtools/api/BamAlgorithms.h +include/bamtools/api/BamAlignment.h +include/bamtools/api/BamAux.h +include/bamtools/api/BamConstants.h +include/bamtools/api/BamIndex.h +include/bamtools/api/BamMultiReader.h +include/bamtools/api/BamReader.h +include/bamtools/api/BamWriter.h +include/bamtools/api/IBamIODevice.h +include/bamtools/api/SamConstants.h +include/bamtools/api/SamHeader.h +include/bamtools/api/SamProgram.h +include/bamtools/api/SamProgramChain.h +include/bamtools/api/SamReadGroup.h +include/bamtools/api/SamReadGroupDictionary.h +include/bamtools/api/SamSequence.h +include/bamtools/api/SamSequenceDictionary.h +include/bamtools/api/algorithms/Sort.h +include/bamtools/api/api_global.h +include/bamtools/shared/bamtools_global.h +lib/libbamtools.so +lib/libbamtools.so.2.5.1 +libdata/pkgconfig/bamtools-1.pc Property changes on: head/biology/bamtools/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