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New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees

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This commit is contained in:
Yuri Victorovich 2019-02-03 20:13:26 +00:00
parent 66e9775902
commit 733be80eb6
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=492071
5 changed files with 127 additions and 0 deletions
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1
biology/Makefile
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@ -43,6 +43,7 @@
SUBDIR += gff2ps
SUBDIR += gmap
SUBDIR += gperiodic
SUBDIR += graphlan
SUBDIR += grappa
SUBDIR += groopm
SUBDIR += hisat2

46
biology/graphlan/Makefile Normal file
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@ -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>

7
biology/graphlan/distinfo Normal file
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@ -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

6
biology/graphlan/pkg-descr Normal file
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@ -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

67
biology/graphlan/pkg-plist Normal file
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@ -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