Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 492070) +++ head/biology/Makefile (revision 492071) @@ -1,155 +1,156 @@ # $FreeBSD$ # COMMENT = Biology 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 += clustalx 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 += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic + SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm 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 += molden SUBDIR += mopac 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-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-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 += 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 += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise .include Index: head/biology/graphlan/Makefile =================================================================== --- head/biology/graphlan/Makefile (nonexistent) +++ head/biology/graphlan/Makefile (revision 492071) @@ -0,0 +1,46 @@ +# $FreeBSD$ + +PORTNAME= graphlan +DISTVERSION= 1.1.3 +CATEGORIES= biology +MASTER_SITES= https://bitbucket.org/${BB_ACCOUNT}/${BB_PROJECT}/get/${BB_COMMIT}${EXTRACT_SUFX}?dummy=/ \ + https://bitbucket.org/${BB_ACCOUNT}/pyphlan/get/eae40ebc0030${EXTRACT_SUFX}?dummy=/:pyphlan \ + https://bitbucket.org/CibioCM/export2graphlan/get/c168a100f37e${EXTRACT_SUFX}?dummy=/:e2g +DISTFILES= ${PORTNAME}-v${DISTVERSION}-${BB_COMMIT}${EXTRACT_SUFX} \ + pyphlan-eae40ebc0030${EXTRACT_SUFX}:pyphlan \ + export2graphlan-c168a100f37e${EXTRACT_SUFX}:e2g + +MAINTAINER= yuri@FreeBSD.org +COMMENT= High-quality circular representations of taxonomic, phylogenetic trees + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/license.txt + +USES= python:2.7 shebangfix +SHEBANG_GLOB= *.py + +BB_ACCOUNT= nsegata +BB_PROJECT= graphlan +BB_COMMIT= 66ec7cfce81e + +WRKSRC= ${WRKDIR}/${BB_ACCOUNT}-${BB_PROJECT}-${BB_COMMIT} + +NO_BUILD= yes +NO_ARCH= yes + +post-extract: + @${CP} -r ${WRKDIR}/${BB_ACCOUNT}-pyphlan* ${WRKSRC}/pyphlan + @${CP} -r ${WRKDIR}/CibioCM-export2graphlan* ${WRKSRC}/export2graphlan + +do-install: + ${CP} -r ${WRKSRC} ${STAGEDIR}${DATADIR} + @cd ${STAGEDIR}${DATADIR} && ${RM} -r examples export2graphlan/examples .hg* license.txt +.for e in ${PORTNAME} ${PORTNAME}_annotate + @(echo "#!/bin/sh"; \ + echo ""; \ + echo ${DATADIR}/${e}.py \"$$\@\"; \ + ) > ${STAGEDIR}${PREFIX}/bin/${e} + @${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${e} +.endfor + +.include Property changes on: head/biology/graphlan/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/graphlan/distinfo =================================================================== --- head/biology/graphlan/distinfo (nonexistent) +++ head/biology/graphlan/distinfo (revision 492071) @@ -0,0 +1,7 @@ +TIMESTAMP = 1549221812 +SHA256 (graphlan-v1.1.3-66ec7cfce81e.tar.gz) = 8931bb166ea46b761d3e1694ff164b82585d5d5ba751ca9cb093bc2fe91c1cb0 +SIZE (graphlan-v1.1.3-66ec7cfce81e.tar.gz) = 2608529 +SHA256 (pyphlan-eae40ebc0030.tar.gz) = 5f9d8e9d8ca5d6c458ba8ce7a7bb2e4a2e9944dc36c6b04850cdcfa4efa046c6 +SIZE (pyphlan-eae40ebc0030.tar.gz) = 27139 +SHA256 (export2graphlan-c168a100f37e.tar.gz) = 7f2738154a9c33c6ab902cc43f498b0bc9a0d038e96154ca0eadef29bc631c6b +SIZE (export2graphlan-c168a100f37e.tar.gz) = 549743 Property changes on: head/biology/graphlan/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/graphlan/pkg-descr =================================================================== --- head/biology/graphlan/pkg-descr (nonexistent) +++ head/biology/graphlan/pkg-descr (revision 492071) @@ -0,0 +1,6 @@ +GraPhlAn is a software tool for producing high-quality circular representations +of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, +informative, and publication-ready representations of phylogenetically- and +taxonomically-driven investigation. + +WWW: https://bitbucket.org/nsegata/graphlan/wiki/Home Property changes on: head/biology/graphlan/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/graphlan/pkg-plist =================================================================== --- head/biology/graphlan/pkg-plist (nonexistent) +++ head/biology/graphlan/pkg-plist (revision 492071) @@ -0,0 +1,67 @@ +bin/graphlan +bin/graphlan_annotate +%%DATADIR%%/export2graphlan/.hg_archival.txt +%%DATADIR%%/export2graphlan/.hgsub +%%DATADIR%%/export2graphlan/.hgsubstate +%%DATADIR%%/export2graphlan/README.md +%%DATADIR%%/export2graphlan/export2graphlan.py +%%DATADIR%%/export2graphlan/license.txt +%%DATADIR%%/export2graphlan/todo-list.txt +%%DATADIR%%/graphlan.py +%%DATADIR%%/graphlan_annotate.py +%%DATADIR%%/pyphlan/.hg_archival.txt +%%DATADIR%%/pyphlan/__init__.py +%%DATADIR%%/pyphlan/bo6_screen.py +%%DATADIR%%/pyphlan/choco_postprocess_euks.py +%%DATADIR%%/pyphlan/choco_postprocess_viruses.py +%%DATADIR%%/pyphlan/choco_profile.py +%%DATADIR%%/pyphlan/choco_summary.py +%%DATADIR%%/pyphlan/conv_cg2cgs.py +%%DATADIR%%/pyphlan/conv_cg2mg.py +%%DATADIR%%/pyphlan/conv_ctxt2coretxt.py +%%DATADIR%%/pyphlan/conv_ctxt2mat.py +%%DATADIR%%/pyphlan/conv_ctxt2rxl.py +%%DATADIR%%/pyphlan/conv_ctxt2ttxt.py +%%DATADIR%%/pyphlan/conv_ctxt2txt.py +%%DATADIR%%/pyphlan/conv_fna2rxl.py +%%DATADIR%%/pyphlan/conv_t2g_2_g2t.py +%%DATADIR%%/pyphlan/conv_tid2tax.py +%%DATADIR%%/pyphlan/conv_txt2ls.py +%%DATADIR%%/pyphlan/conv_uc2txt.py +%%DATADIR%%/pyphlan/fna_exact_matches.py +%%DATADIR%%/pyphlan/fna_extract_from_bo6.py +%%DATADIR%%/pyphlan/fna_extract_from_primersearch.py +%%DATADIR%%/pyphlan/fna_extract_with_primers.py +%%DATADIR%%/pyphlan/fna_g2r.py +%%DATADIR%%/pyphlan/fna_len.py +%%DATADIR%%/pyphlan/fna_revcomp.py +%%DATADIR%%/pyphlan/fna_sss.py +%%DATADIR%%/pyphlan/fna_t2g.py +%%DATADIR%%/pyphlan/libsvm_cv.py +%%DATADIR%%/pyphlan/license.txt +%%DATADIR%%/pyphlan/merg_ctxt.py +%%DATADIR%%/pyphlan/mlst_table2fna.py +%%DATADIR%%/pyphlan/msg.py +%%DATADIR%%/pyphlan/pyphlan.py +%%DATADIR%%/pyphlan/tab.py +%%DATADIR%%/pyphlan/tab.pyc +%%DATADIR%%/pyphlan/tab_sel_cols.py +%%DATADIR%%/pyphlan/tab_sub.py +%%DATADIR%%/pyphlan/tree_cores.py +%%DATADIR%%/pyphlan/tree_get_leaves.py +%%DATADIR%%/pyphlan/tree_get_subtrees.py +%%DATADIR%%/pyphlan/tree_markers.py +%%DATADIR%%/pyphlan/tree_pairwisedists.py +%%DATADIR%%/pyphlan/tree_precision.py +%%DATADIR%%/pyphlan/tree_prune.py +%%DATADIR%%/pyphlan/tree_recall.py +%%DATADIR%%/pyphlan/tree_rename.py +%%DATADIR%%/pyphlan/tree_reroot.py +%%DATADIR%%/pyphlan/tree_select_markers.py +%%DATADIR%%/pyphlan/tree_subtree.py +%%DATADIR%%/pyphlan/util_argparse.py +%%DATADIR%%/pyphlan/utils.py +%%DATADIR%%/readme.txt +%%DATADIR%%/src/__init__.py +%%DATADIR%%/src/graphlan_lib.py +%%DATADIR%%/src/pyphlan.py Property changes on: head/biology/graphlan/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