Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 502127) +++ head/biology/Makefile (revision 502128) @@ -1,166 +1,167 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed 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 += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm 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 += 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-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 += 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-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython 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 += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/mothur/Makefile =================================================================== --- head/biology/mothur/Makefile (nonexistent) +++ head/biology/mothur/Makefile (revision 502128) @@ -0,0 +1,33 @@ +# $FreeBSD$ + +PORTNAME= mothur +DISTVERSIONPREFIX= v +DISTVERSION= 1.42.1-3 +DISTVERSIONSUFFIX= -gb670137a +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Software for bioinformatics of the microbial ecology community + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +BUILD_DEPENDS= bash:shells/bash + +USES= gmake localbase readline shebangfix +SHEBANG_FILES= source/uchime_src/mk +USE_GITHUB= yes +ALL_TARGET= ${PORTNAME} + +BINARY_ALIAS= g++=${CXX} + +EXES= ${PORTNAME} uchime + +PLIST_FILES= ${EXES:S/^/bin\//} + +do-install: # https://github.com/mothur/mothur/issues/615 +.for e in ${EXES} + ${INSTALL_PROGRAM} ${WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin +.endfor + +.include Property changes on: head/biology/mothur/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/mothur/distinfo =================================================================== --- head/biology/mothur/distinfo (nonexistent) +++ head/biology/mothur/distinfo (revision 502128) @@ -0,0 +1,3 @@ +TIMESTAMP = 1558374468 +SHA256 (mothur-mothur-v1.42.1-3-gb670137a_GH0.tar.gz) = fe7742102af4eb62fef75357b3a2563283e70f8ec344898f7c4396ff41309bf1 +SIZE (mothur-mothur-v1.42.1-3-gb670137a_GH0.tar.gz) = 1651578 Property changes on: head/biology/mothur/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/mothur/pkg-descr =================================================================== --- head/biology/mothur/pkg-descr (nonexistent) +++ head/biology/mothur/pkg-descr (revision 502128) @@ -0,0 +1,4 @@ +This project seeks to develop a single piece of open-source, expandable software +to fill the bioinformatics needs of the microbial ecology community. + +WWW: https://www.mothur.org/ Property changes on: head/biology/mothur/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