Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 470581) +++ head/biology/Makefile (revision 470582) @@ -1,140 +1,141 @@ # $FreeBSD$ # 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 += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += crux 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 += 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 += pbbam SUBDIR += pbcopper SUBDIR += pbseqan 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 += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/clustal-omega/Makefile =================================================================== --- head/biology/clustal-omega/Makefile (nonexistent) +++ head/biology/clustal-omega/Makefile (revision 470582) @@ -0,0 +1,20 @@ +# $FreeBSD$ + +PORTNAME= clustal-omega +DISTVERSION= 1.2.4 +CATEGORIES= biology +MASTER_SITES= http://www.clustal.org/omega/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Multiple alignment of nucleic acid and protein, replaces clustalw + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libargtable2.so:devel/argtable + +USES= libtool localbase + +GNU_CONFIGURE= yes + +.include Property changes on: head/biology/clustal-omega/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/clustal-omega/distinfo =================================================================== --- head/biology/clustal-omega/distinfo (nonexistent) +++ head/biology/clustal-omega/distinfo (revision 470582) @@ -0,0 +1,3 @@ +TIMESTAMP = 1526846209 +SHA256 (clustal-omega-1.2.4.tar.gz) = 8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee +SIZE (clustal-omega-1.2.4.tar.gz) = 1170516 Property changes on: head/biology/clustal-omega/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/clustal-omega/pkg-descr =================================================================== --- head/biology/clustal-omega/pkg-descr (nonexistent) +++ head/biology/clustal-omega/pkg-descr (revision 470582) @@ -0,0 +1,8 @@ +Clustal Omega is the latest addition to the Clustal family. It offers a +significant increase in scalability over previous versions, allowing hundreds +of thousands of sequences to be aligned in only a few hours. It will also make +use of multiple processors, where present. In addition, the quality of +alignments is superior to previous versions, as measured by a range of popular +benchmarks. + +WWW: http://www.clustal.org/omega/ Property changes on: head/biology/clustal-omega/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/clustal-omega/pkg-plist =================================================================== --- head/biology/clustal-omega/pkg-plist (nonexistent) +++ head/biology/clustal-omega/pkg-plist (revision 470582) @@ -0,0 +1,32 @@ +bin/clustalo +include/clustalo/clustal-omega-config.h +include/clustalo/clustal-omega.h +include/clustalo/clustal/hhalign_wrapper.h +include/clustalo/clustal/ktuple_pair.h +include/clustalo/clustal/log.h +include/clustalo/clustal/mbed.h +include/clustalo/clustal/muscle_tree.h +include/clustalo/clustal/pair_dist.h +include/clustalo/clustal/progress.h +include/clustalo/clustal/seq.h +include/clustalo/clustal/symmatrix.h +include/clustalo/clustal/tree.h +include/clustalo/clustal/util.h +include/clustalo/clustal/weights.h +include/clustalo/hhalign/general.h +include/clustalo/hhalign/hhfunc.h +include/clustalo/squid/gki.h +include/clustalo/squid/gsi64.h +include/clustalo/squid/msa.h +include/clustalo/squid/rk.h +include/clustalo/squid/sqfuncs.h +include/clustalo/squid/squid.h +include/clustalo/squid/sre_random.h +include/clustalo/squid/ssi.h +include/clustalo/squid/stockholm.h +include/clustalo/squid/stopwatch.h +include/clustalo/squid/vectorops.h +include/clustalo/squid/version.h +lib/libclustalo.a +libdata/pkgconfig/clustalo.pc +%%DOCSDIR%%/README Property changes on: head/biology/clustal-omega/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