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biology/njplot: Revive and update to version 2.4
Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8518
This commit is contained in:
Joseph Mingrone
parent
bb94ef0d66
commit
a3fc357457
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=426241
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@ -7966,7 +7966,6 @@ cad/slffea||2015-11-28|Has expired: Broken for more than 6 months
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audio/cripple||2015-11-28|Has expired: Broken for more than 6 months
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cad/geda-gattrib||2015-11-28|Has expired: Broken for more than 6 months
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cad/findhier||2015-11-28|Has expired: Broken for more than 6 months
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biology/njplot||2015-11-28|Has expired: Broken for more than 6 months
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audio/wmmp||2015-11-28|Has expired: Broken for more than 6 months
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x11/avant-window-navigator||2015-11-28|Has expired: Broken for more than 6 months
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cad/geda-netlist||2015-11-28|Has expired: Broken for more than 6 months
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@ -55,6 +55,7 @@
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SUBDIR += muscle
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SUBDIR += ncbi-blast+
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SUBDIR += ncbi-toolkit
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SUBDIR += njplot
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SUBDIR += p5-AcePerl
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SUBDIR += p5-Bio-ASN1-EntrezGene
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SUBDIR += p5-Bio-Das
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39
biology/njplot/Makefile
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biology/njplot/Makefile
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# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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# $FreeBSD$
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PORTNAME= njplot
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PORTVERSION= 2.4
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CATEGORIES= biology
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MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/ \
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ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/
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MAINTAINER= jrm@FreeBSD.org
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COMMENT= Phylogenetic tree drawing program
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LICENSE= NONE
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BUILD_DEPENDS= blastall:biology/ncbi-toolkit
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MAKEFILE= makefile
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USES= motif
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USE_XORG= x11 xmu xp xt
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BINARIES= newicktops newicktotxt njplot unrooted
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PLIST_FILES= ${BINARIES:S|^|bin/|} man/man1/njplot.1.gz \
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man/man1/unrooted.1.gz ${DATADIR}/njplot.help
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PORTDOCS= njplot.html njplot.gif
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OPTIONS_DEFINE= DOCS
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do-install:
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${INSTALL_PROGRAM} ${BINARIES:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
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${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MANPREFIX}/man/man1
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@${MKDIR} ${STAGEDIR}${DATADIR}
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${INSTALL_DATA} ${WRKSRC}/njplot.help ${STAGEDIR}${DATADIR}
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do-install-DOCS-on:
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@${MKDIR} ${STAGEDIR}${DOCSDIR}
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${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}
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.include <bsd.port.mk>
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3
biology/njplot/distinfo
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biology/njplot/distinfo
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@ -0,0 +1,3 @@
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TIMESTAMP = 1479168824
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SHA256 (njplot-2.4.tar.gz) = e470f7583691da2ad36a7cda4269bf64807f77cb27fe1e16cbfefc45942469d3
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SIZE (njplot-2.4.tar.gz) = 83239
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biology/njplot/files/patch-makefile
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biology/njplot/files/patch-makefile
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--- makefile.orig 2012-01-04 08:50:43 UTC
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+++ makefile
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@@ -1,5 +1,5 @@
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#uncomment and locally adapt next line to fix the full helpfile path name
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-HELPFILENAME = -DHELPFILENAME=\"/usr/share/njplot/njplot.help\"
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+HELPFILENAME = -DHELPFILENAME=\"${DATADIR}/njplot.help\"
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#comment out next line and uncomment next 2 to use the PDFLib Lite library
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NO_PDF = -DNO_PDF
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@@ -7,27 +7,31 @@ NO_PDF = -DNO_PDF
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#PDFLIB = -L$(PDF) -lpdf
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# c compiler and linker
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-CC = gcc
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+CC ?= cc
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-# Vibrant top directory
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-VIBRANT = /usr/include/ncbi
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+NCBIINC = $(LOCALBASE)/include/ncbi
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+NCBILIB = $(LOCALBASE)/lib/ncbi
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OBJECTS = njplot-vib.o
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OBJUNROOTED = unrooted-vib.o preptree.o
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+CFLAGS = -c -DWIN_MOTIF -Dunix -I${LOCALBASE}/include -I$(NCBIINC) $(HELPFILENAME) $(NO_PDF) -Wimplicit-function-declaration
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-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT) $(HELPFILENAME) $(NO_PDF)
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-
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all: njplot unrooted newicktops newicktotxt
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njplot : $(OBJECTS)
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$(CC) -o njplot $(OBJECTS) \
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- -lvibrant -lncbi -lXm -lXt
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-
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+ -L$(NCBILIB) \
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+ -lvibrant -lncbi \
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+ $(MOTIFLIB) \
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+ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm
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+
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unrooted : $(OBJUNROOTED)
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$(CC) -o unrooted $(OBJUNROOTED) \
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- -lvibrant -lncbi -lXm -lXt
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+ -L$(NCBILIB) -lvibrant -lncbi \
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+ $(MOTIFLIB) \
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+ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm
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newicktops: njplot-vib.c
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$(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm
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17
biology/njplot/pkg-descr
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biology/njplot/pkg-descr
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NJplot is a tree drawing program able to draw any phylogenetic tree expressed
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in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
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package). NJplot is especially convenient for rooting the unrooted trees
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obtained from parsimony, distance or maximum likelihood tree-building methods.
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The package contains the following programs:
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njplot - draw phylogenetic trees and interactively modify them
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newicktops - non-interactive version rendering into a PostScript file
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newicktotxt - non-interactive version rendering into a text file
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unrooted - draw unrooted circular trees
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If you use NJplot in a published work, please cite the following reference:
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Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
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biological sequence banks. Biochimie, 78, 364-369.
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WWW: http://pbil.univ-lyon1.fr/software/njplot.html
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