Date: Wed, 5 Dec 2007 04:41:45 GMT From: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/118438: New port: biology/njplot Phylogenetic tree drawing program Message-ID: <200712050441.lB54fjoW027647@www.freebsd.org> Resent-Message-ID: <200712050450.lB54o0AL005965@freefall.freebsd.org>
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>Number: 118438 >Category: ports >Synopsis: New port: biology/njplot Phylogenetic tree drawing program >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Dec 05 04:50:00 UTC 2007 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: >Organization: >Environment: >Description: NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. WWW: http://pbil.univ-lyon1.fr/software/njplot.html Although there are no explicit licensing statements fot NJplot, the submitter has confirmed by e-mail to the author that it can be redistributed in source and in binary forms without restrictions. The package contains 4 programs: njplot, newicktops, newicktotxt, unrooted. If -DWITHOUT_X11 is specified, 2 non-interactive programs (newickto{ps,txt}) will be built. >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # biology/njplot # biology/njplot/Makefile # biology/njplot/distinfo # biology/njplot/files # biology/njplot/files/patch-makefile # biology/njplot/pkg-descr # echo c - biology/njplot mkdir -p biology/njplot > /dev/null 2>&1 echo x - biology/njplot/Makefile sed 's/^X//' >biology/njplot/Makefile << 'END-of-biology/njplot/Makefile' X# New ports collection makefile for: njplot X# Date created: 5 December 2007 X# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> X# X# $FreeBSD$ X# X XPORTNAME= njplot XPORTVERSION= 2.1 XCATEGORIES= biology XMASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/ XDISTFILES= ${PORTNAME}${EXTRACT_SUFX} X XMAINTAINER= mzaki@biol.s.u-tokyo.ac.jp XCOMMENT= Phylogenetic tree drawing program capable of interactive manupilation X X.ifndef (WITHOUT_X11) XBUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit XUSE_XLIB= yes XUSE_MOTIF= yes X.endif X XMAKEFILE= makefile X XBINARIES= newicktops newicktotxt X.ifndef (WITHOUT_X11) XBINARIES+= njplot unrooted X.endif X.for file in ${BINARIES} XPLIST_FILES+= bin/${file} X.endfor X XPORTDOCS= njplot.help njplot.html njplot.gif X XMAN1= njplot.1 unrooted.1 X X.ifdef (WITHOUT_X11) Xpost-patch: X ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile X.endif X Xdo-install: X.for file in ${BINARIES} X ${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin X.endfor X.for file in ${MAN1} X ${INSTALL_MAN} ${WRKSRC}/${file} ${PREFIX}/man/man1 X.endfor X.if !defined(NOPORTDOCS) X ${MKDIR} ${DOCSDIR} X.for file in ${PORTDOCS} X ${INSTALL_MAN} ${WRKSRC}/${file} ${DOCSDIR} X.endfor X.endif X X.include <bsd.port.mk> END-of-biology/njplot/Makefile echo x - biology/njplot/distinfo sed 's/^X//' >biology/njplot/distinfo << 'END-of-biology/njplot/distinfo' XMD5 (njplot.tar.gz) = d98adc1e624e8fcc8cc86e7dfe65e67c XSHA256 (njplot.tar.gz) = dd8a54c3903cd104d8322257a87b5fbf3afb7776a96fcf9bee504ae1ad54c0c1 XSIZE (njplot.tar.gz) = 85735 END-of-biology/njplot/distinfo echo c - biology/njplot/files mkdir -p biology/njplot/files > /dev/null 2>&1 echo x - biology/njplot/files/patch-makefile sed 's/^X//' >biology/njplot/files/patch-makefile << 'END-of-biology/njplot/files/patch-makefile' X--- makefile.orig Thu Oct 11 01:54:00 2007 X+++ makefile Mon Dec 3 22:08:28 2007 X@@ -1,5 +1,5 @@ X #uncomment and locally adapt next line to fix the full helpfile path name X-HELPFILENAME = -DHELPFILENAME=\"/usr/share/njplot/njplot.help\" X+HELPFILENAME = -DHELPFILENAME=\"$(LOCALBASE)/doc/njplot/njplot.help\" X X #comment out next line and uncomment next 2 to use the PDFLib Lite library X NO_PDF = -DNO_PDF X@@ -7,43 +7,45 @@ X #PDFLIB = -L$(PDF) -lpdf X X # c compiler and linker X-CC = gcc X+CC ?= gcc X X # Vibrant top directory X-VIBRANT = /banques0/ncbiJun04 X+#VIBRANT = /banques0/ncbiJun04 X+NCBIINC = $(LOCALBASE)/include/ncbi X+NCBILIB = $(LOCALBASE)/lib/ncbi X X X # X11 include directory X-X11INCL = /usr/X11R6/include X+X11INCL = $(X11BASE)/include X X # motif library directory X-MOTIFLIB = /sw/lib X-MOTIFINCL = /sw/include X+#MOTIFLIB = /sw/lib X+#MOTIFINCL = /sw/include X X OBJECTS = njplot-vib.o X OBJUNROOTED = unrooted-vib.o preptree.o X X X-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ X- -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ X- -Wimplicit-function-declaration -g X+CFLAGS = -c -DWIN_MOTIF -Dunix -I$(NCBIINC) \ X+ -I$(X11INCL) $(HELPFILENAME) $(NO_PDF) \ X+ -Wimplicit-function-declaration X X all: njplot unrooted newicktops newicktotxt X X X njplot : $(OBJECTS) X $(CC) -g -o njplot $(OBJECTS) \ X- -L$(VIBRANT)/lib \ X+ -L$(NCBILIB) \ X -lvibrant -lncbi \ X $(PDFLIB) \ X- -L$(MOTIFLIB) -lXm \ X- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm X+ $(MOTIFLIB) \ X+ -L$(X11BASE)/lib -lXmu -lXt -lX11 -lm X X unrooted : $(OBJUNROOTED) X $(CC) -g -o unrooted $(OBJUNROOTED) \ X- -L$(VIBRANT)/lib -lvibrant -lncbi \ X- -L$(MOTIFLIB) -lXm \ X- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm X+ -L$(NCBILIB) -lvibrant -lncbi \ X+ $(MOTIFLIB) \ X+ -L$(X11BASE)/lib -lXmu -lXt -lX11 -lm X X newicktops: njplot-vib.c X $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm END-of-biology/njplot/files/patch-makefile echo x - biology/njplot/pkg-descr sed 's/^X//' >biology/njplot/pkg-descr << 'END-of-biology/njplot/pkg-descr' XNJplot is a tree drawing program able to draw any phylogenetic tree expressed Xin the Newick phylogenetic tree format (e.g., the format used by the PHYLIP Xpackage). NJplot is especially convenient for rooting the unrooted trees Xobtained from parsimony, distance or maximum likelihood tree-building methods. X XThe package contains the following programs: Xnjplot - draw phylogenetic trees and interactively modify them Xnewicktops - non-interactive version rendering into a PostScript file Xnewicktotxt - non-interactive version rendering into a text file Xunrooted - draw unrooted circular trees X XIf you use NJplot in a published work, please cite the following reference: X XPerriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for Xbiological sequence banks. Biochimie, 78, 364-369. X XWWW: http://pbil.univ-lyon1.fr/software/njplot.html END-of-biology/njplot/pkg-descr exit >Release-Note: >Audit-Trail: >Unformatted:
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