diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/njplot/Makefile | 55 | ||||
| -rw-r--r-- | biology/njplot/distinfo | 3 | ||||
| -rw-r--r-- | biology/njplot/files/patch-makefile | 69 | ||||
| -rw-r--r-- | biology/njplot/pkg-descr | 17 |
5 files changed, 145 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 1baefa585e00..a9e3ab465a60 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -52,6 +52,7 @@ SUBDIR += muscle SUBDIR += nab SUBDIR += ncbi-toolkit + SUBDIR += njplot SUBDIR += ortep3 SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene diff --git a/biology/njplot/Makefile b/biology/njplot/Makefile new file mode 100644 index 000000000000..9e118db518cb --- /dev/null +++ b/biology/njplot/Makefile @@ -0,0 +1,55 @@ +# New ports collection makefile for: njplot +# Date created: 5 December 2007 +# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> +# +# $FreeBSD$ +# + +PORTNAME= njplot +PORTVERSION= 2.1 +CATEGORIES= biology +MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/ + +MAINTAINER= mzaki@biol.s.u-tokyo.ac.jp +COMMENT= Phylogenetic tree drawing program capable of interactive manipulation + +.ifndef (WITHOUT_X11) +BUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit +USE_XLIB= yes +USE_MOTIF= yes +.endif + +MAKEFILE= makefile + +BINARIES= newicktops newicktotxt +.ifndef (WITHOUT_X11) +BINARIES+= njplot unrooted +.endif +.for file in ${BINARIES} +PLIST_FILES+= bin/${file} +.endfor + +PORTDOCS= njplot.help njplot.html njplot.gif + +MAN1= njplot.1 unrooted.1 + +.ifdef (WITHOUT_X11) +post-patch: + ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile +.endif + +do-install: +.for file in ${BINARIES} + ${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin +.endfor +.for file in ${MAN1} + ${INSTALL_MAN} ${WRKSRC}/${file} ${PREFIX}/man/man1 +.endfor +.if !defined(NOPORTDOCS) + ${MKDIR} ${DOCSDIR} +.for file in ${PORTDOCS} + ${INSTALL_MAN} ${WRKSRC}/${file} ${DOCSDIR} +.endfor +.endif + +.include <bsd.port.mk> diff --git a/biology/njplot/distinfo b/biology/njplot/distinfo new file mode 100644 index 000000000000..74d09b4c0b59 --- /dev/null +++ b/biology/njplot/distinfo @@ -0,0 +1,3 @@ +MD5 (njplot-2.1.tar.gz) = d98adc1e624e8fcc8cc86e7dfe65e67c +SHA256 (njplot-2.1.tar.gz) = dd8a54c3903cd104d8322257a87b5fbf3afb7776a96fcf9bee504ae1ad54c0c1 +SIZE (njplot-2.1.tar.gz) = 85735 diff --git a/biology/njplot/files/patch-makefile b/biology/njplot/files/patch-makefile new file mode 100644 index 000000000000..448fbe7d41be --- /dev/null +++ b/biology/njplot/files/patch-makefile @@ -0,0 +1,69 @@ +--- makefile.orig Thu Oct 11 01:54:00 2007 ++++ makefile Mon Dec 3 22:08:28 2007 +@@ -1,5 +1,5 @@ + #uncomment and locally adapt next line to fix the full helpfile path name +-HELPFILENAME = -DHELPFILENAME=\"/usr/share/njplot/njplot.help\" ++HELPFILENAME = -DHELPFILENAME=\"$(LOCALBASE)/doc/njplot/njplot.help\" + + #comment out next line and uncomment next 2 to use the PDFLib Lite library + NO_PDF = -DNO_PDF +@@ -7,43 +7,45 @@ + #PDFLIB = -L$(PDF) -lpdf + + # c compiler and linker +-CC = gcc ++CC ?= gcc + + # Vibrant top directory +-VIBRANT = /banques0/ncbiJun04 ++#VIBRANT = /banques0/ncbiJun04 ++NCBIINC = $(LOCALBASE)/include/ncbi ++NCBILIB = $(LOCALBASE)/lib/ncbi + + + # X11 include directory +-X11INCL = /usr/X11R6/include ++X11INCL = $(LOCALBASE)/include + + # motif library directory +-MOTIFLIB = /sw/lib +-MOTIFINCL = /sw/include ++#MOTIFLIB = /sw/lib ++#MOTIFINCL = /sw/include + + OBJECTS = njplot-vib.o + OBJUNROOTED = unrooted-vib.o preptree.o + + +-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ +- -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ +- -Wimplicit-function-declaration -g ++CFLAGS = -c -DWIN_MOTIF -Dunix -I$(NCBIINC) \ ++ -I$(X11INCL) $(HELPFILENAME) $(NO_PDF) \ ++ -Wimplicit-function-declaration + + all: njplot unrooted newicktops newicktotxt + + + njplot : $(OBJECTS) + $(CC) -g -o njplot $(OBJECTS) \ +- -L$(VIBRANT)/lib \ ++ -L$(NCBILIB) \ + -lvibrant -lncbi \ + $(PDFLIB) \ +- -L$(MOTIFLIB) -lXm \ +- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm ++ $(MOTIFLIB) \ ++ -L$(X11BASE)/lib -lXmu -lXt -lX11 -lm + + unrooted : $(OBJUNROOTED) + $(CC) -g -o unrooted $(OBJUNROOTED) \ +- -L$(VIBRANT)/lib -lvibrant -lncbi \ +- -L$(MOTIFLIB) -lXm \ +- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm ++ -L$(NCBILIB) -lvibrant -lncbi \ ++ $(MOTIFLIB) \ ++ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm + + newicktops: njplot-vib.c + $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm diff --git a/biology/njplot/pkg-descr b/biology/njplot/pkg-descr new file mode 100644 index 000000000000..679993f19121 --- /dev/null +++ b/biology/njplot/pkg-descr @@ -0,0 +1,17 @@ +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. + +The package contains the following programs: +njplot - draw phylogenetic trees and interactively modify them +newicktops - non-interactive version rendering into a PostScript file +newicktotxt - non-interactive version rendering into a text file +unrooted - draw unrooted circular trees + +If you use NJplot in a published work, please cite the following reference: + +Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for +biological sequence banks. Biochimie, 78, 364-369. + +WWW: http://pbil.univ-lyon1.fr/software/njplot.html |