ports/118438: New port: biology/njplot Phylogenetic tree drawing program

Wed Dec 5 04:50:01 UTC 2007

>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 at 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 at 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: