Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 537925) +++ head/biology/Makefile (revision 537926) @@ -1,178 +1,179 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper 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-Bio-Variation 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 += plink SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch + SUBDIR += vt SUBDIR += wise .include Index: head/biology/vt/Makefile =================================================================== --- head/biology/vt/Makefile (nonexistent) +++ head/biology/vt/Makefile (revision 537926) @@ -0,0 +1,27 @@ +# $FreeBSD$ + +PORTNAME= vt +DISTVERSION= 0.57721 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Discovers short variants from Next Generation Sequencing data + +LICENSE= MIT + +LIB_DEPENDS= libhts.so:biology/htslib \ + libsvm.so:science/libsvm \ + libdeflate.so:archivers/libdeflate \ + libcurl.so:ftp/curl + +USES= gmake ssl +USE_GITHUB= yes + +GH_ACCOUNT= atks + +PLIST_FILES= bin/vt + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/vt ${STAGEDIR}${PREFIX}/bin + +.include Property changes on: head/biology/vt/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/vt/distinfo =================================================================== --- head/biology/vt/distinfo (nonexistent) +++ head/biology/vt/distinfo (revision 537926) @@ -0,0 +1,3 @@ +TIMESTAMP = 1591286057 +SHA256 (atks-vt-0.57721_GH0.tar.gz) = 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17 +SIZE (atks-vt-0.57721_GH0.tar.gz) = 20925247 Property changes on: head/biology/vt/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/vt/files/patch-Makefile =================================================================== --- head/biology/vt/files/patch-Makefile (nonexistent) +++ head/biology/vt/files/patch-Makefile (revision 537926) @@ -0,0 +1,41 @@ +--- Makefile.orig 2018-05-09 00:33:23 UTC ++++ Makefile +@@ -1,7 +1,8 @@ +-OPTFLAG = -O3 +-INCLUDES = -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 +-CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS +-CXX = g++ ++# ${LOCALBASE}/include must come after bundled dirs ++INCLUDES = -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I${LOCALBASE}/include ++CXXFLAGS ?= -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS ++CXXFLAGS += -std=c++0x $(INCLUDES) -D__STDC_LIMIT_MACROS ++CXX ?= g++ + + SOURCESONLY = + +@@ -139,11 +140,11 @@ SOURCESONLY = main.cpp + TARGET = vt + TOOLSRC = $(SOURCES:=.cpp) $(SOURCESONLY) + TOOLOBJ = $(TOOLSRC:.cpp=.o) +-LIBDEFLATE = lib/libdeflate/libdeflate.a +-LIBHTS = lib/htslib/libhts.a ++LIBDEFLATE = -ldeflate ++LIBHTS = -lhts + LIBRMATH = lib/Rmath/libRmath.a + LIBPCRE2 = lib/pcre2/libpcre2.a +-LIBSVM = lib/libsvm/libsvm.a ++LIBSVM = -lsvm + + all : $(TARGET) + +@@ -165,8 +166,8 @@ ${LIBSVM} : + version : + git rev-parse HEAD | cut -c 1-8 | awk '{print "#define VERSION \"0.5772-"$$0"\""}' > version.h; + +-$(TARGET) : ${LIBHTS} ${LIBRMATH} ${LIBPCRE2} ${LIBSVM} $(TOOLOBJ) +- $(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto ++$(TARGET) : ${LIBRMATH} ${LIBPCRE2} $(TOOLOBJ) ++ $(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) -L${LOCALBASE}/lib $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto + + $(TOOLOBJ): $(HEADERSONLY) + Property changes on: head/biology/vt/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/vt/files/patch-lib_Rmath_Make.inc =================================================================== --- head/biology/vt/files/patch-lib_Rmath_Make.inc (nonexistent) +++ head/biology/vt/files/patch-lib_Rmath_Make.inc (revision 537926) @@ -0,0 +1,31 @@ +--- lib/Rmath/Make.inc.orig 2020-06-04 16:21:07 UTC ++++ lib/Rmath/Make.inc +@@ -3,21 +3,21 @@ + OS = $(shell uname) + ARCH = $(shell uname -m) + +-FC = gfortran +-FFLAGS-add += -O3 ++FC ?= gfortran ++# FFLAGS-add += -O3 + +-USEGCC = 1 +-USECLANG = 0 ++USEGCC = 0 ++USECLANG = 1 + +-CFLAGS-add += -Wall -O3 ++# CFLAGS-add += -Wall -O3 + + ifeq ($(USECLANG),1) + USEGCC = 0 +-CC = clang ++CC ?= clang + endif + + ifeq ($(USEGCC),1) +-CC = gcc ++CC ?= gcc + endif + AR = ar + Property changes on: head/biology/vt/files/patch-lib_Rmath_Make.inc ___________________________________________________________________ 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/vt/files/patch-lib_pcre2_Makefile =================================================================== --- head/biology/vt/files/patch-lib_pcre2_Makefile (nonexistent) +++ head/biology/vt/files/patch-lib_pcre2_Makefile (revision 537926) @@ -0,0 +1,11 @@ +--- lib/pcre2/Makefile.orig 2020-06-04 16:13:50 UTC ++++ lib/pcre2/Makefile +@@ -28,7 +28,7 @@ TOOLSRC = $(SOURCES:=.c) + TOOLOBJ = $(TOOLSRC:.c=.o) + + .c.o : +- gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o $@ -c $*.c ++ ${CC} ${CFLAGS} -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o $@ -c $*.c + + libpcre2.a: $(TOOLOBJ) + @-rm -f $@ Property changes on: head/biology/vt/files/patch-lib_pcre2_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/vt/files/patch-svm__predict.h =================================================================== --- head/biology/vt/files/patch-svm__predict.h (nonexistent) +++ head/biology/vt/files/patch-svm__predict.h (revision 537926) @@ -0,0 +1,14 @@ +--- svm_predict.h.orig 2020-06-04 16:33:17 UTC ++++ svm_predict.h +@@ -25,8 +25,8 @@ + #define SVM_PREDICT_H + + #include "program.h" +-#include "libsvm/svm.h" ++#include + + void svm_predict(int argc, char ** argv); + +-#endif +\ No newline at end of file ++#endif Property changes on: head/biology/vt/files/patch-svm__predict.h ___________________________________________________________________ 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/vt/files/patch-svm__train.h =================================================================== --- head/biology/vt/files/patch-svm__train.h (nonexistent) +++ head/biology/vt/files/patch-svm__train.h (revision 537926) @@ -0,0 +1,15 @@ +--- svm_train.h.orig 2020-06-04 16:32:44 UTC ++++ svm_train.h +@@ -25,9 +25,9 @@ + #define SVM_TRAIN_H + + #include "program.h" +-#include "libsvm/svm.h" ++#include + #include "Rmath/Rmath.h" + + void svm_train(int argc, char ** argv); + +-#endif +\ No newline at end of file ++#endif Property changes on: head/biology/vt/files/patch-svm__train.h ___________________________________________________________________ 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/vt/pkg-descr =================================================================== --- head/biology/vt/pkg-descr (nonexistent) +++ head/biology/vt/pkg-descr (revision 537926) @@ -0,0 +1,4 @@ +vt is a variant tool set that discovers short variants from Next Generation +Sequencing data. + +WWW: https://genome.sph.umich.edu/wiki/Vt Property changes on: head/biology/vt/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