diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/seaview/Makefile | 10 | ||||
| -rw-r--r-- | biology/seaview/distinfo | 2 | ||||
| -rw-r--r-- | biology/seaview/files/patch-aa | 39 | ||||
| -rw-r--r-- | biology/seaview/files/patch-align.cxx | 18 | ||||
| -rw-r--r-- | biology/seaview/files/patch-chooser_plus.cxx | 20 | ||||
| -rw-r--r-- | biology/seaview/pkg-comment | 2 | ||||
| -rw-r--r-- | biology/seaview/pkg-descr | 10 | ||||
| -rw-r--r-- | biology/seaview/pkg-plist | 1 |
8 files changed, 72 insertions, 30 deletions
diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile index a4e06a6157fc..21df6296c076 100644 --- a/biology/seaview/Makefile +++ b/biology/seaview/Makefile @@ -6,26 +6,26 @@ # PORTNAME= seaview -PORTVERSION= 1.0 +PORTVERSION= 2002.10.18 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ DISTNAME= ${PORTNAME} EXTRACT_SUFX= .tar -MAINTAINER= frankch@waru.life.nthu.edu.tw +MAINTAINER= ports@FreeBSD.org -BROKEN= "Checksum is incorrect" - -LIB_DEPENDS= forms.1:${PORTSDIR}/x11-toolkits/xforms +LIB_DEPENDS= fltk.1:${PORTSDIR}/x11-toolkits/fltk USE_X_PREFIX= YES NO_WRKSUBDIR= YES EXTRACT_CMD= ${TAR} EXTRACT_BEFORE_ARGS= -xf EXTRACT_AFTER_ARGS= # empty +MAKEFILE= makefile do-install: @ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin + @ ${INSTALL_SCRIPT} ${WRKSRC}/seaview_align.sh ${PREFIX}/bin @ (${MKDIR} ${PREFIX}/lib/X11/seaview) @ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview diff --git a/biology/seaview/distinfo b/biology/seaview/distinfo index 28018709d128..866bdaf801e9 100644 --- a/biology/seaview/distinfo +++ b/biology/seaview/distinfo @@ -1 +1 @@ -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab +MD5 (seaview.tar) = 1f9b5157966b98f2724428d3fb1f6b17 diff --git a/biology/seaview/files/patch-aa b/biology/seaview/files/patch-aa index b326a5a807a0..fdca7da38e5f 100644 --- a/biology/seaview/files/patch-aa +++ b/biology/seaview/files/patch-aa @@ -1,20 +1,23 @@ ---- Makefile.orig Mon Aug 30 20:54:56 1999 -+++ Makefile Mon Aug 30 20:55:48 1999 -@@ -0,0 +1,17 @@ -+#matpt.h -+#seaview.h -+CC ?= gcc -+CFLAGS+= -I${X11BASE}/include -+LIBS = -L${X11BASE}/lib -lxforms -lX11 -lm -+SRCS = align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c -+OBJS = align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o +--- makefile.orig Wed Sep 25 23:58:15 2002 ++++ makefile Mon Nov 18 11:26:42 2002 +@@ -1,13 +1,15 @@ +-FLTK = ../fltk-1.1.0 ++OPT = -O2 + +-OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o old_file_chooser.o ++OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o + +-CFLAGS = -c $(OPT) -I$(FLTK) ++CFLAGS = -c $(OPT) -I$(PREFIX)/include + +-CXX = CC ++CXX = g++ + +all: seaview -+ -+seaview: $(OBJS) -+ $(CC) -o seaview $(OBJS) $(LIBS) -+ -+c.o.: $(SRCS) -+ $(CC) $(CFLAGS) -c $(SRCS) -+ -+ + + seaview : $(OBJECTS) +- $(CXX) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk -lX11 -lm ++ $(CXX) -o $@ $(OBJECTS) -L$(PREFIX)/lib -lfltk -lX11 -lMesaGL -lXext -lm + + + .SUFFIXES: .cxx .h .o diff --git a/biology/seaview/files/patch-align.cxx b/biology/seaview/files/patch-align.cxx new file mode 100644 index 000000000000..9947269dd135 --- /dev/null +++ b/biology/seaview/files/patch-align.cxx @@ -0,0 +1,18 @@ +--- align.cxx.orig Tue Oct 8 19:43:40 2002 ++++ align.cxx Mon Nov 18 11:40:08 2002 +@@ -1,5 +1,6 @@ + #include "seaview.h" + #include <stdlib.h> ++#include <unistd.h> + #include <ctype.h> + #ifndef WIN32 + #include <FL/x.H> +@@ -155,7 +156,7 @@ + #endif + debut = view->active_region->list->debut; + fin = view->active_region->list->fin; +-tmpnam(base_fname); ++mkstemp(base_fname); + /* + convertir en minuscules car clustalw n'accepte pas les majuscules ds filenames + */ diff --git a/biology/seaview/files/patch-chooser_plus.cxx b/biology/seaview/files/patch-chooser_plus.cxx new file mode 100644 index 000000000000..fe62a4edf2d6 --- /dev/null +++ b/biology/seaview/files/patch-chooser_plus.cxx @@ -0,0 +1,20 @@ +--- chooser_plus.cxx.orig Mon Nov 18 11:14:10 2002 ++++ chooser_plus.cxx Mon Nov 18 11:17:52 2002 +@@ -442,7 +442,7 @@ + strcmp(pat,f->browser.pattern))) { + // if pattern is different, remove name but leave old directory: + const char* p = f->input.value(); +- const char* q = fl_filename_name(p); ++ const char* q = filename_name(p); + f->input.value(p, q-p); + } + f->browser.pattern = pat; +@@ -500,7 +500,7 @@ + strcmp(pat,f->browser.pattern))) { + // if pattern is different, remove name but leave old directory: + const char* p = f->input.value(); +- const char* q = fl_filename_name(p); ++ const char* q = filename_name(p); + f->input.value(p, q-p); + } + f->browser.pattern = pat; diff --git a/biology/seaview/pkg-comment b/biology/seaview/pkg-comment index 624e358fd953..7cee832df80f 100644 --- a/biology/seaview/pkg-comment +++ b/biology/seaview/pkg-comment @@ -1 +1 @@ -Multiple DNA sequence alignment editor +Multiple DNA/protein sequence alignment editor diff --git a/biology/seaview/pkg-descr b/biology/seaview/pkg-descr index 351ecddde5b1..19847132b9ae 100644 --- a/biology/seaview/pkg-descr +++ b/biology/seaview/pkg-descr @@ -1,15 +1,15 @@ -Seaview is a multiple DNA sequence alignment editor. -You can align DNA sequences from several organisms, and find out their +Seaview is a multiple sequence alignment editor. +You can align DNA/protein sequences from several organisms, and find out their relative postions in phylogenic tree. -File test.mase can be used as an example file. Open the on-line help window through button 'Help' to learn seaview usage. +Example mase files could be found at: -WWW: http://pbil.univ-lyon1.fr/software/seaview.html + ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ ***************************************************************************** * The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ . -* Add an entry in your Xresources or Xdefaults file with: +* Add an entry in your .Xresources or .Xdefaults file with: * * seaview*helpfile: /usr/X11R6/lib/X11/seaview/seaview.help ***************************************************************************** diff --git a/biology/seaview/pkg-plist b/biology/seaview/pkg-plist index b4a419f0bd9f..6f5cd13faa7e 100644 --- a/biology/seaview/pkg-plist +++ b/biology/seaview/pkg-plist @@ -1,3 +1,4 @@ bin/seaview +bin/seaview_align.sh lib/X11/seaview/seaview.help @dirrm lib/X11/seaview |