6 files changed, 127 insertions, 8 deletions

diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index 5cedd67f3f54..88e69e65ba72 100644
--- a/biology/clustalw/Makefile
+++ b/biology/clustalw/Makefile
@@ -9,18 +9,19 @@ PORTNAME=	clustalw
 PORTVERSION=	1.81
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
-DISTNAME=	clustalw1.81.UNIX
+DISTNAME=	${PORTNAME}${PORTVERSION}.UNIX
 
 MAINTAINER=	dbader@eece.unm.edu
 
+PORTREVISION=	1
 WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
 
-do-build:
-		cd ${WRKSRC} ; ${MAKE} -f makefile
+MAKEFILE=	makefile
+ALL_TARGET=	# empty
 
 do-install:
-		${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
-		${MKDIR} ${PREFIX}/share/${PORTNAME}
-		${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME}
+	${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
+	@${MKDIR} ${PREFIX}/share/${PORTNAME}
+	${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME}
 
 .include <bsd.port.mk>
diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa
index d404277773d9..56e36ffce6ba 100644
--- a/biology/clustalw/files/patch-aa
+++ b/biology/clustalw/files/patch-aa
@@ -5,7 +5,7 @@
          char *help_file_name = "clustalw.hlp";
  #else
 -        char *help_file_name = "clustalw_help";
-+        char *help_file_name = "/usr/local/share/clustalw/clustalw_help";
++        char *help_file_name = DATADIR "/clustalw_help";
  #endif
  
  sint max_names; /* maximum length of names in current alignment file */
diff --git a/biology/clustalw/files/patch-ab b/biology/clustalw/files/patch-ab
new file mode 100644
index 000000000000..03e9eccaae85
--- /dev/null
+++ b/biology/clustalw/files/patch-ab
@@ -0,0 +1,15 @@
+--- makefile.orig	Wed Jun  7 16:55:06 2000
++++ makefile	Tue Aug  8 02:30:53 2000
+@@ -10,9 +10,9 @@
+ 
+ HEADERS = general.h clustalw.h
+ 
+-CC	= cc
+-CFLAGS  = -c -O
+-LFLAGS	= -O -lm 
++CC	?= cc
++CFLAGS  += -c -DDATADIR=\"${PREFIX}/share/clustalw\"
++LFLAGS	= -lm 
+ 
+ clustalw : $(OBJECTS) amenu.o clustalw.o
+ 	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
diff --git a/biology/clustalw/files/patch-ac b/biology/clustalw/files/patch-ac
new file mode 100644
index 000000000000..9ac14ac11427
--- /dev/null
+++ b/biology/clustalw/files/patch-ac
@@ -0,0 +1,74 @@
+--- interface.c.orig	Wed Jun  7 16:50:07 2000
++++ interface.c	Tue Aug  8 03:11:33 2000
+@@ -1078,7 +1078,7 @@
+ 	/* added for File System Standards  - Francois */
+ 	path1=(char *)ckalloc((strlen(path)+64)*sizeof(char));
+ 	strcpy(path1,path);
+-	strcat(path1,"/usr/share/clustalx:/usr/local/share/clustalx"); 
++	strcat(path1,DATADIR); 
+ 
+         lf=(sint)strlen(fname);
+         deb=path1;
+@@ -2121,7 +2121,7 @@
+ 			strcpy(local_prompt,"\n\nEnter new name to avoid overwriting ");
+ 			strcat(local_prompt," [%s]: ");          
+ 			fprintf(stdout,local_prompt,file_name);
+-			gets(temp);
++			fgets(temp,sizeof(temp),stdin);
+ 			if(*temp != EOS) strcpy(file_name,temp);
+ 		}
+ 	}
+@@ -2129,7 +2129,7 @@
+ 		strcpy(local_prompt,prompt);
+ 		strcat(local_prompt," [%s]: ");          
+ 		fprintf(stdout,local_prompt,file_name);
+-		gets(temp);
++		fgets(temp,sizeof(temp),stdin);
+ 		if(*temp != EOS) strcpy(file_name,temp);
+ 	}
+ 
+@@ -2335,7 +2335,7 @@
+ 		if (usemenu)
+             	fprintf(stdout,"\nUse the existing GUIDE TREE file,  %s  (y/n) ? [y]: ",
+                                            tree_name);
+-                gets(temp);
++                fgets(temp,sizeof(temp),stdin);
+                 if(*temp != 'n' && *temp != 'N') {
+                     strcpy(phylip_name,tree_name);
+                     use_tree = TRUE;
+@@ -2567,7 +2567,7 @@
+ 
+             fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ",
+                                            phylip_name);
+-                	gets(temp);
++                	fgets(temp,sizeof(temp),stdin);
+                 	if(*temp != EOS)
+                         	strcpy(phylip_name,temp);
+         	}
+@@ -2676,7 +2676,7 @@
+ #endif
+             	fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1,  %s  (y/n) ? [y]: ",
+                                            tree_name);
+-                gets(temp);
++                fgets(temp,sizeof(temp),stdin);
+                 if(*temp != 'n' && *temp != 'N') {
+                     strcpy(p1_tree_name,tree_name);
+                     use_tree1 = TRUE;
+@@ -2702,7 +2702,7 @@
+ #endif
+             	fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2,  %s  (y/n) ? [y]: ",
+                                            tree_name);
+-                gets(temp);
++                fgets(temp,sizeof(temp),stdin);
+                 if(*temp != 'n' && *temp != 'N') {
+                     strcpy(p2_tree_name,tree_name);
+                     use_tree2 = TRUE;
+@@ -3730,7 +3730,7 @@
+ 	if(usemenu) {
+         	fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ",
+                                            parname);
+-               	gets(temp);
++               	fgets(temp,sizeof(temp),stdin);
+                	if(*temp != EOS)
+                        	strcpy(parname,temp);
+        	}
diff --git a/biology/clustalw/files/patch-ad b/biology/clustalw/files/patch-ad
new file mode 100644
index 000000000000..da64accff072
--- /dev/null
+++ b/biology/clustalw/files/patch-ad
@@ -0,0 +1,29 @@
+--- util.c.orig	Wed Jun  7 16:50:08 2000
++++ util.c	Tue Aug  8 02:59:43 2000
+@@ -174,7 +174,7 @@
+ void getstr(char *instr,char *outstr)
+ {	
+ 	fprintf(stdout,"%s: ",instr);
+-	gets(outstr);
++	fgets(outstr,sizeof(outstr),stdin);
+ }
+ 
+ double getreal(char *instr,double minx,double maxx,double def)
+@@ -185,7 +185,7 @@
+ 	
+ 	while(TRUE) {
+ 		fprintf(stdout,"%s (%.1f-%.1f)   [%.1f]: ",instr,minx,maxx,def);
+-		gets(line);
++		fgets(line,sizeof(line),stdin);
+ 		status=sscanf(line,"%f",&ret);
+ 		if(status == EOF) return def;
+ 		if(ret>maxx) {
+@@ -210,7 +210,7 @@
+ 	while(TRUE) {
+ 		fprintf(stdout,"%s (%d..%d)    [%d]: ",
+ 		instr,(pint)minx,(pint)maxx,(pint)def);
+-		gets(line);
++		fgets(line,sizeof(line),stdin);
+ 		status=sscanf(line,"%d",&ret);
+ 		if(status == EOF) return def;
+ 		if(ret>maxx) {
diff --git a/biology/clustalw/pkg-descr b/biology/clustalw/pkg-descr
index fcb3931270b0..f63c0c96b776 100644
--- a/biology/clustalw/pkg-descr
+++ b/biology/clustalw/pkg-descr
@@ -21,4 +21,4 @@ weight matrix choice. Nucleic Acids Research 22: 4673-4680.
 CLUSTAL for multiple sequence alignments. Methods in Enzymology 266:
 383-402.
 
-  See URL: www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
+WWW: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html