Date: Sun, 3 Feb 2019 20:13:26 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r492071 - in head/biology: . graphlan Message-ID: <201902032013.x13KDQ1O088765@repo.freebsd.org>
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Author: yuri Date: Sun Feb 3 20:13:26 2019 New Revision: 492071 URL: https://svnweb.freebsd.org/changeset/ports/492071 Log: New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees Added: head/biology/graphlan/ head/biology/graphlan/Makefile (contents, props changed) head/biology/graphlan/distinfo (contents, props changed) head/biology/graphlan/pkg-descr (contents, props changed) head/biology/graphlan/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Feb 3 20:07:40 2019 (r492070) +++ head/biology/Makefile Sun Feb 3 20:13:26 2019 (r492071) @@ -43,6 +43,7 @@ SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic + SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += hisat2 Added: head/biology/graphlan/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/graphlan/Makefile Sun Feb 3 20:13:26 2019 (r492071) @@ -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 <bsd.port.mk> Added: head/biology/graphlan/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/graphlan/distinfo Sun Feb 3 20:13:26 2019 (r492071) @@ -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 Added: head/biology/graphlan/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/graphlan/pkg-descr Sun Feb 3 20:13:26 2019 (r492071) @@ -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 Added: head/biology/graphlan/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/graphlan/pkg-plist Sun Feb 3 20:13:26 2019 (r492071) @@ -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
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