Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 467484) +++ head/biology/Makefile (revision 467485) @@ -1,130 +1,131 @@ # $FreeBSD$ # 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 += fastahack 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 += pear-merger 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 += 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 += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/fastahack/Makefile =================================================================== --- head/biology/fastahack/Makefile (nonexistent) +++ head/biology/fastahack/Makefile (revision 467485) @@ -0,0 +1,19 @@ +# $FreeBSD$ + +PORTNAME= fastahack +DISTVERSION= g20160702 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Utility for indexing and sequence extraction from FASTA files + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= ekg +GH_TAGNAME= bbc645f2f7966cb7b44446200c02627c3168b399 + +MAKEFILE= ${FILESDIR}/Makefile +INSTALL_TARGET= install-strip + +.include Property changes on: head/biology/fastahack/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/fastahack/distinfo =================================================================== --- head/biology/fastahack/distinfo (nonexistent) +++ head/biology/fastahack/distinfo (revision 467485) @@ -0,0 +1,3 @@ +TIMESTAMP = 1523600462 +SHA256 (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = dc8ef61765b7720fd2d163143696f1c82251bfd906ac5261642e7230d81d5da6 +SIZE (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = 18200 Property changes on: head/biology/fastahack/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/fastahack/files/Makefile =================================================================== --- head/biology/fastahack/files/Makefile (nonexistent) +++ head/biology/fastahack/files/Makefile (revision 467485) @@ -0,0 +1,62 @@ + +# Use ?= to allow overriding from the env or command-line, e.g. +# +# make CXXFLAGS="-O3 -fPIC" install +# +# Package managers will override many of these variables automatically, so +# this is aimed at making it easy to create packages (Debian packages, +# FreeBSD ports, MacPorts, pkgsrc, etc.) + +CXX ?= c++ +CXXFLAGS ?= -O3 +DESTDIR ?= stage +PREFIX ?= /usr/local +STRIP ?= strip +INSTALL ?= install -c +MKDIR ?= mkdir -p +AR ?= ar + +# Required flags that we shouldn't override +# Must be compiler-independent +CXXFLAGS += -D_FILE_OFFSET_BITS=64 + +BIN = fastahack +LIB = libfastahack.a +OBJS = Fasta.o split.o disorder.o +MAIN = FastaHack.o + +all: $(BIN) $(LIB) + +$(BIN): $(OBJS) $(MAIN) + $(CXX) $(CXXFLAGS) $(OBJS) $(MAIN) -o $(BIN) + +$(LIB): $(OBJS) + ${AR} -rs $(LIB) $(OBJS) + +FastaHack.o: Fasta.h FastaHack.cpp + $(CXX) $(CXXFLAGS) -c FastaHack.cpp + +Fasta.o: Fasta.h Fasta.cpp + $(CXX) $(CXXFLAGS) -c Fasta.cpp + +split.o: split.h split.cpp + $(CXX) $(CXXFLAGS) -c split.cpp + +disorder.o: disorder.c disorder.h + $(CXX) $(CXXFLAGS) -c disorder.c + +install: all + $(MKDIR) $(DESTDIR)$(PREFIX)/bin + $(MKDIR) $(DESTDIR)$(PREFIX)/include/fastahack + $(MKDIR) $(DESTDIR)$(PREFIX)/lib + $(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin + $(INSTALL) *.h $(DESTDIR)$(PREFIX)/include/fastahack + $(INSTALL) $(LIB) $(DESTDIR)$(PREFIX)/lib + +install-strip: install + $(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) + +clean: + rm -rf $(BIN) $(LIB) $(OBJS) $(DESTDIR) + +.PHONY: clean Property changes on: head/biology/fastahack/files/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/fastahack/pkg-descr =================================================================== --- head/biology/fastahack/pkg-descr (nonexistent) +++ head/biology/fastahack/pkg-descr (revision 467485) @@ -0,0 +1,7 @@ +Fastahack is a small application for indexing and extracting sequences and +subsequences from FASTA files. The included Fasta.cpp library provides a FASTA +reader and indexer that can be embedded into applications which would benefit +from directly reading subsequences from FASTA files. The library automatically +handles index file generation and use. + +WWW: https://github.com/ekg/fastahack Property changes on: head/biology/fastahack/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/fastahack/pkg-plist =================================================================== --- head/biology/fastahack/pkg-plist (nonexistent) +++ head/biology/fastahack/pkg-plist (revision 467485) @@ -0,0 +1,7 @@ +bin/fastahack +include/fastahack/Fasta.h +include/fastahack/LargeFileSupport.h +include/fastahack/Region.h +include/fastahack/disorder.h +include/fastahack/split.h +lib/libfastahack.a Property changes on: head/biology/fastahack/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