svn commit: r492071 - in head/biology: . graphlan
Yuri Victorovich
yuri at FreeBSD.org
Sun Feb 3 20:13:28 UTC 2019
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 at 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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