Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 504267) +++ head/biology/Makefile (revision 504268) @@ -1,169 +1,170 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm 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 += cufflinks 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 += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/treekin/Makefile =================================================================== --- head/biology/treekin/Makefile (nonexistent) +++ head/biology/treekin/Makefile (revision 504268) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= treekin +DISTVERSION= 0.5.1 +CATEGORIES= biology +MASTER_SITES= https://www.tbi.univie.ac.at/RNA/packages/source/ +DISTNAME= Treekin-${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Efficient computation of RNA folding dynamics + +LICENSE= LatticeLib +LICENSE_NAME= LatticeLib Disclaimer and Copyright +LICENSE_FILE= ${WRKSRC}/COPYING +LICENSE_PERMS= auto-accept dist-mirror pkg-mirror + +BUILD_DEPENDS= lapacke>0:math/lapacke + +USES= blaslapack:netlib fortran gmake localbase:ldflags + +GNU_CONFIGURE= yes + +BINARY_ALIAS= make=${GMAKE} + +PLIST_FILES= bin/${PORTNAME} \ + man/man1/${PORTNAME}.1.gz + +.include Property changes on: head/biology/treekin/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/treekin/distinfo =================================================================== --- head/biology/treekin/distinfo (nonexistent) +++ head/biology/treekin/distinfo (revision 504268) @@ -0,0 +1,3 @@ +TIMESTAMP = 1560629735 +SHA256 (Treekin-0.5.1.tar.gz) = aae56c1a746829b02a9b97c6a54d1d58348718d4ca585ef41a5dbdd41d5c9f06 +SIZE (Treekin-0.5.1.tar.gz) = 222232 Property changes on: head/biology/treekin/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/treekin/pkg-descr =================================================================== --- head/biology/treekin/pkg-descr (nonexistent) +++ head/biology/treekin/pkg-descr (revision 504268) @@ -0,0 +1,5 @@ +treekin computes folding dynamics on coarse grained version of an energy +landscape, where all conformations belonging to the same local minimum have +been contracted into a single macro-state. + +WWW: https://www.tbi.univie.ac.at/RNA/Treekin/ Property changes on: head/biology/treekin/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