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Code Issues Releases Activity

- Support CC/CFLAGS/PREFIX properly

Browse Source 
- gets() -> fgets()
- Add WWW: line into pkg/DESCR

Also bumped PORTREVISION to 1

PR:		21572
Submitted by:	tkato@prontomail.ne.jp <KATO@FreeBSD.ORG, Tsuguru@FreeBSD.ORG>
Reviewed by:	will
Approved by:	MAINTAINER (dbader@eece.unm.edu)
This commit is contained in:
James E. Housley 2000-10-03 01:10:19 +00:00
parent 6f3b4bd632
commit 52b82e19ed
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=33343
6 changed files with 127 additions and 8 deletions
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13
biology/clustalw/Makefile
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@ -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>

2
biology/clustalw/files/patch-aa
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@ -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 */

15
biology/clustalw/files/patch-ab Normal file
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@ -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)

74
biology/clustalw/files/patch-ac Normal file
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@ -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);
}

29
biology/clustalw/files/patch-ad Normal file
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@ -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) {

2
biology/clustalw/pkg-descr
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@ -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