Page MenuHomeFreeBSD
Files F105939968

D8518.diff
No OneTemporary
Actions

D8518.diff
View Options

Index: head/MOVED
===================================================================
--- head/MOVED
+++ head/MOVED
@@ -7966,7 +7966,6 @@
audio/cripple||2015-11-28|Has expired: Broken for more than 6 months
cad/geda-gattrib||2015-11-28|Has expired: Broken for more than 6 months
cad/findhier||2015-11-28|Has expired: Broken for more than 6 months
-biology/njplot||2015-11-28|Has expired: Broken for more than 6 months
audio/wmmp||2015-11-28|Has expired: Broken for more than 6 months
x11/avant-window-navigator||2015-11-28|Has expired: Broken for more than 6 months
cad/geda-netlist||2015-11-28|Has expired: Broken for more than 6 months
Index: head/biology/Makefile
===================================================================
--- head/biology/Makefile
+++ head/biology/Makefile
@@ -55,6 +55,7 @@
SUBDIR += muscle
SUBDIR += ncbi-blast+
SUBDIR += ncbi-toolkit
+ SUBDIR += njplot
SUBDIR += p5-AcePerl
SUBDIR += p5-Bio-ASN1-EntrezGene
SUBDIR += p5-Bio-Das
Index: head/biology/njplot/Makefile
===================================================================
--- head/biology/njplot/Makefile
+++ head/biology/njplot/Makefile
@@ -0,0 +1,39 @@
+# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
+# $FreeBSD$
+
+PORTNAME= njplot
+PORTVERSION= 2.4
+CATEGORIES= biology
+MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/ \
+ ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/
+
+MAINTAINER= jrm@FreeBSD.org
+COMMENT= Phylogenetic tree drawing program
+
+LICENSE= NONE
+
+BUILD_DEPENDS= blastall:biology/ncbi-toolkit
+
+MAKEFILE= makefile
+
+USES= motif
+USE_XORG= x11 xmu xp xt
+
+BINARIES= newicktops newicktotxt njplot unrooted
+PLIST_FILES= ${BINARIES:S|^|bin/|} man/man1/njplot.1.gz \
+ man/man1/unrooted.1.gz ${DATADIR}/njplot.help
+PORTDOCS= njplot.html njplot.gif
+
+OPTIONS_DEFINE= DOCS
+
+do-install:
+ ${INSTALL_PROGRAM} ${BINARIES:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
+ ${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MANPREFIX}/man/man1
+ @${MKDIR} ${STAGEDIR}${DATADIR}
+ ${INSTALL_DATA} ${WRKSRC}/njplot.help ${STAGEDIR}${DATADIR}
+
+do-install-DOCS-on:
+ @${MKDIR} ${STAGEDIR}${DOCSDIR}
+ ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}
+
+.include <bsd.port.mk>
Index: head/biology/njplot/distinfo
===================================================================
--- head/biology/njplot/distinfo
+++ head/biology/njplot/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1479168824
+SHA256 (njplot-2.4.tar.gz) = e470f7583691da2ad36a7cda4269bf64807f77cb27fe1e16cbfefc45942469d3
+SIZE (njplot-2.4.tar.gz) = 83239
Index: head/biology/njplot/files/patch-makefile
===================================================================
--- head/biology/njplot/files/patch-makefile
+++ head/biology/njplot/files/patch-makefile
@@ -0,0 +1,49 @@
+--- makefile.orig 2012-01-04 08:50:43 UTC
++++ makefile
+@@ -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=\"${DATADIR}/njplot.help\"
+
+ #comment out next line and uncomment next 2 to use the PDFLib Lite library
+ NO_PDF = -DNO_PDF
+@@ -7,27 +7,31 @@ NO_PDF = -DNO_PDF
+ #PDFLIB = -L$(PDF) -lpdf
+
+ # c compiler and linker
+-CC = gcc
++CC ?= cc
+
+-# Vibrant top directory
+-VIBRANT = /usr/include/ncbi
++NCBIINC = $(LOCALBASE)/include/ncbi
++NCBILIB = $(LOCALBASE)/lib/ncbi
+
+ OBJECTS = njplot-vib.o
+ OBJUNROOTED = unrooted-vib.o preptree.o
+
++CFLAGS = -c -DWIN_MOTIF -Dunix -I${LOCALBASE}/include -I$(NCBIINC) $(HELPFILENAME) $(NO_PDF) -Wimplicit-function-declaration
+
+-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT) $(HELPFILENAME) $(NO_PDF)
+-
+ all: njplot unrooted newicktops newicktotxt
+
+
+ njplot : $(OBJECTS)
+ $(CC) -o njplot $(OBJECTS) \
+- -lvibrant -lncbi -lXm -lXt
+-
++ -L$(NCBILIB) \
++ -lvibrant -lncbi \
++ $(MOTIFLIB) \
++ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm
++
+ unrooted : $(OBJUNROOTED)
+ $(CC) -o unrooted $(OBJUNROOTED) \
+- -lvibrant -lncbi -lXm -lXt
++ -L$(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
Index: head/biology/njplot/pkg-descr
===================================================================
--- head/biology/njplot/pkg-descr
+++ head/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

File Metadata

Mime Type
text/plain
Expires
Mon, Dec 23, 8:35 PM (18 h, 58 m)
Storage Engine
blob
Storage Format
Raw Data
Storage Handle
15580025
Default Alt Text
D8518.diff (5 KB)

Event Timeline