Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 474557) +++ head/biology/Makefile (revision 474558) @@ -1,144 +1,145 @@ # $FreeBSD$ # 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 += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss + SUBDIR += exonerate 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 += igv 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-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics 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 += stringtie 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/exonerate/Makefile =================================================================== --- head/biology/exonerate/Makefile (nonexistent) +++ head/biology/exonerate/Makefile (revision 474558) @@ -0,0 +1,22 @@ +# Created by: Motomichi Matsuzaki +# $FreeBSD$ + +PORTNAME= exonerate +PORTVERSION= 2.4.0 +CATEGORIES= biology +MASTER_SITES= http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/ + +MAINTAINER= mzaki@niid.go.jp +COMMENT= Generic tool for sequence alignment + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= gnome pkgconfig +GNU_CONFIGURE= yes +USE_GNOME= glib20 +TEST_TARGET= check + +MAKE_JOBS_UNSAFE= yes + +.include Property changes on: head/biology/exonerate/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/exonerate/distinfo =================================================================== --- head/biology/exonerate/distinfo (nonexistent) +++ head/biology/exonerate/distinfo (revision 474558) @@ -0,0 +1,3 @@ +TIMESTAMP = 1529394154 +SHA256 (exonerate-2.4.0.tar.gz) = f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 +SIZE (exonerate-2.4.0.tar.gz) = 520899 Property changes on: head/biology/exonerate/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/exonerate/pkg-descr =================================================================== --- head/biology/exonerate/pkg-descr (nonexistent) +++ head/biology/exonerate/pkg-descr (revision 474558) @@ -0,0 +1,10 @@ +Exonerate is a tool for various types of pairwise sequence comparison. +It allows us to align sequences using many alignment models including +est2genome, protein2genome, and so on. + +Citation: + +Slater, G. S. C. and Birney, E. (2005) Automated generation of heuristics +for biological sequence comparison. BMC Bioinformatics 6:31. + +WWW: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Property changes on: head/biology/exonerate/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/exonerate/pkg-plist =================================================================== --- head/biology/exonerate/pkg-plist (nonexistent) +++ head/biology/exonerate/pkg-plist (revision 474558) @@ -0,0 +1,31 @@ +bin/exonerate +bin/ipcress +bin/exonerate-server +bin/fastaclean +bin/fastaclip +bin/fastachecksum +bin/fastacomposition +bin/fastadiff +bin/fastaexplode +bin/fastafetch +bin/fastahardmask +bin/fastaindex +bin/fastalength +bin/fastanrdb +bin/fastaoverlap +bin/fastareformat +bin/fastaremove +bin/fastarevcomp +bin/fastasoftmask +bin/fastasort +bin/fastasplit +bin/fastasubseq +bin/fastatranslate +bin/fastavalidcds +bin/fasta2esd +bin/fastaannotatecdna +bin/esd2esi +man/man1/exonerate-server.1.gz +man/man1/fastautils.1.gz +man/man1/exonerate.1.gz +man/man1/ipcress.1.gz Property changes on: head/biology/exonerate/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