Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 470574) +++ head/biology/Makefile (revision 470575) @@ -1,139 +1,140 @@ # $FreeBSD$ # 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 += 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/clustalx/Makefile =================================================================== --- head/biology/clustalx/Makefile (nonexistent) +++ head/biology/clustalx/Makefile (revision 470575) @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= clustalx +DISTVERSION= 2.1 +CATEGORIES= biology +MASTER_SITES= http://www.clustal.org/download/current/ \ + ftp://ftp.ebi.ac.uk/pub/software/clustalw2/${DISTVERSION}/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Multiple alignment of nucleic acid and protein sequences with GUI + +LICENSE= LGPL3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= qmake +USE_QT4= corelib gui moc qmake_build xml + +PLIST_FILES= bin/clustalx \ + ${DATADIR}/colprot.xml \ + ${DATADIR}/coldna.xml \ + ${DATADIR}/colprint.xml \ + ${DATADIR}/clustalx.hlp + +post-patch: + @${REINPLACE_CMD} -e 's|col.*.xml|${DATADIR}/&|' \ + ${WRKSRC}/ClustalQtParams.h + @${REINPLACE_CMD} -e 's|clustalx.hlp|${DATADIR}/&|' \ + ${WRKSRC}/HelpDisplayWidget.cpp + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/clustalx ${STAGEDIR}${PREFIX}/bin + @${MKDIR} ${STAGEDIR}${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/col*.xml ${WRKSRC}/clustalx.hlp \ + ${STAGEDIR}${DATADIR} + +.include Property changes on: head/biology/clustalx/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/clustalx/distinfo =================================================================== --- head/biology/clustalx/distinfo (nonexistent) +++ head/biology/clustalx/distinfo (revision 470575) @@ -0,0 +1,3 @@ +TIMESTAMP = 1526839706 +SHA256 (clustalx-2.1.tar.gz) = e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 +SIZE (clustalx-2.1.tar.gz) = 341649 Property changes on: head/biology/clustalx/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/clustalx/files/patch-clustalW_general_VectorOutOfRange.h =================================================================== --- head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h (nonexistent) +++ head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h (revision 470575) @@ -0,0 +1,11 @@ +--- clustalW/general/VectorOutOfRange.h.orig 2018-05-20 18:08:08 UTC ++++ clustalW/general/VectorOutOfRange.h +@@ -5,6 +5,8 @@ + */ + #include + #include ++#include ++ + namespace clustalw + { + Property changes on: head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.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/clustalx/pkg-descr =================================================================== --- head/biology/clustalx/pkg-descr (nonexistent) +++ head/biology/clustalx/pkg-descr (revision 470575) @@ -0,0 +1,8 @@ +ClustalX is the graphical version of Clustal, a general purpose multiple +sequence alignment program for DNA or proteins. It produces biologically +meaningful multiple sequence alignments of divergent sequences. It calculates +the best match for the selected sequences, and lines them up so that the +identities, similarities and differences can be seen. Evolutionary +relationships can be seen via viewing Cladograms or Phylograms. + +WWW: http://www.clustal.org/ Property changes on: head/biology/clustalx/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