1
0
mirror of https://git.FreeBSD.org/ports.git synced 2025-01-07 06:40:06 +00:00

Remove biology/njplot

The author of both NJplot and SeaView says that NJplot can be considered
deprecated and replaced by SeaView.
This commit is contained in:
Joseph Mingrone 2018-12-11 15:04:12 +00:00
parent b753dc567d
commit a65cd96f01
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=487239
6 changed files with 1 additions and 111 deletions

1
MOVED
View File

@ -10781,3 +10781,4 @@ sysutils/gnome-device-manager||2018-12-11|Has expired: GNOME 2 application
sysutils/battfink||2018-12-11|Has expired: GNOME 2 application
sysutils/cog||2018-12-11|Has expired: GNOME 2 application
sysutils/gcdmaster||2018-12-11|Has expired: GNOME 2 application
biology/njplot|biology/seaview|2018-12-11|Has expired: Deprecated by upstream; use biology/seaview instead

View File

@ -71,7 +71,6 @@
SUBDIR += ncbi-cxx-toolkit
SUBDIR += ncbi-toolkit
SUBDIR += ngs-sdk
SUBDIR += njplot
SUBDIR += p5-AcePerl
SUBDIR += p5-Bio-ASN1-EntrezGene
SUBDIR += p5-Bio-Coordinate

View File

@ -1,41 +0,0 @@
# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
# $FreeBSD$
PORTNAME= njplot
PORTVERSION= 2.4
CATEGORIES= biology
MASTER_SITES= http://awarnach.mathstat.dal.ca/distfiles/ \
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
PORTDATA= 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>

View File

@ -1,3 +0,0 @@
TIMESTAMP = 1479168824
SHA256 (njplot-2.4.tar.gz) = e470f7583691da2ad36a7cda4269bf64807f77cb27fe1e16cbfefc45942469d3
SIZE (njplot-2.4.tar.gz) = 83239

View File

@ -1,49 +0,0 @@
--- 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

View File

@ -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