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authorJames E. Housley <jeh@FreeBSD.org>2000-10-03 01:10:19 +0000
committerJames E. Housley <jeh@FreeBSD.org>2000-10-03 01:10:19 +0000
commit52b82e19ed7bc691bd4e23b88c7744590a78f0f0 (patch)
treeb31e9108a84a3cb540123e134ec1313051472330 /biology
parent6f3b4bd632d38ab5af521351ac548f1086418d7f (diff)
downloadports-52b82e19ed7bc691bd4e23b88c7744590a78f0f0.tar.gz
ports-52b82e19ed7bc691bd4e23b88c7744590a78f0f0.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/clustalw/Makefile13
-rw-r--r--biology/clustalw/files/patch-aa2
-rw-r--r--biology/clustalw/files/patch-ab15
-rw-r--r--biology/clustalw/files/patch-ac74
-rw-r--r--biology/clustalw/files/patch-ad29
-rw-r--r--biology/clustalw/pkg-descr2
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