diff options
Diffstat (limited to 'biology/njplot')
| -rw-r--r-- | biology/njplot/Makefile | 55 | ||||
| -rw-r--r-- | biology/njplot/distinfo | 2 | ||||
| -rw-r--r-- | biology/njplot/files/patch-makefile | 69 | ||||
| -rw-r--r-- | biology/njplot/pkg-descr | 17 |
4 files changed, 0 insertions, 143 deletions
diff --git a/biology/njplot/Makefile b/biology/njplot/Makefile deleted file mode 100644 index 3003037..0000000 --- a/biology/njplot/Makefile +++ /dev/null @@ -1,55 +0,0 @@ -# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> -# $FreeBSD$ - -PORTNAME= njplot -PORTVERSION= 2.1 -PORTREVISION= 3 -CATEGORIES= biology -MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/ - -MAINTAINER= mzaki@m.u-tokyo.ac.jp -COMMENT= Phylogenetic tree drawing program capable of interactive manipulation - -BROKEN= Unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2015-11-26 - -OPTIONS_DEFINE= DOCS X11 -OPTIONS_DEFAULT= DOCS X11 - -.include <bsd.port.options.mk> - -.if ${PORT_OPTIONS:MX11} -BUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit -USE_XORG= x11 xt xmu xp -USES= motif -.endif - -MAKEFILE= makefile - -BINARIES= newicktops newicktotxt -.if ${PORT_OPTIONS:MX11} -BINARIES+= njplot unrooted -.endif -.for file in ${BINARIES} -PLIST_FILES+= bin/${file} -.endfor - -PORTDOCS= njplot.help njplot.html njplot.gif - -MAN_1= njplot.1 unrooted.1 -PLIST_FILES+= man/man1/njplot.1.gz \ - man/man1/unrooted.1.gz - -.if !${PORT_OPTIONS:MX11} -post-patch: - ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile -.endif - -do-install: - ${INSTALL_PROGRAM} ${BINARIES:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin - ${INSTALL_MAN} ${MAN_1:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/man/man1 - ${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_MAN} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} - -.include <bsd.port.mk> diff --git a/biology/njplot/distinfo b/biology/njplot/distinfo deleted file mode 100644 index 7e5cae2..0000000 --- a/biology/njplot/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -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 deleted file mode 100644 index 2f913de..0000000 --- a/biology/njplot/files/patch-makefile +++ /dev/null @@ -1,69 +0,0 @@ ---- 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 -+ $(MOTIFLIB) \ -+ -L$(LOCALBASE)/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 deleted file mode 100644 index 679993f..0000000 --- a/biology/njplot/pkg-descr +++ /dev/null @@ -1,17 +0,0 @@ -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 |
