add: use shell to set env

shell/bap

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/bap

shell/dap

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/dap

shell/mep

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/mep

shell/nipf

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPNIP=/usr/share/staden-lg/help/dap_help NIPHELP=/usr/share/staden-lg/help/NIP.HLP NIPHPNT=/usr/share/staden-lg/help/NIP.PNT NIPMARG=/usr/share/staden-lg/help/NIP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/nipf

shell/sap

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/sap

shell/xbap

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xbap

shell/xdap

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xdap

shell/xmep

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xmep

shell/xsap

@@ -0,0 +1,2 @@
+#!/bin/bash
+env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xsap

src/abi/makefile-alpha

@@ -5,7 +5,8 @@
 #
 # Programs made by this makefile
 #
-PROGS = getABISampleName
+PROGS = getABISampleName 2rs
+all: $(PROGS)
 
 #
 # Where the wild things are
@@ -26,6 +27,8 @@ LDFLAGS = -g
 getABISampleName: getABISampleName.o
 	$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
 
+2rs: 2rs.o
+	$(LD) $(LDFLAGS) -o 2rs 2rs.o
 
 #
 # Special dependencies

src/cop/makefile-alpha

@@ -6,7 +6,7 @@
 # Programs made by this makefile
 #
 PROGS = cop cop-bap
-
+all: $(PROGS)
 #
 # Where the wild things are
 #

src/getMCH/makefile-alpha

@@ -23,7 +23,7 @@
 # Programs made by this makefile
 #
 PROGS = getMCH trace2seq
-
+all: $(PROGS)
 #
 # Where the wild things are
 #

src/indexseqlibs/excludewords.c

@@ -13,7 +13,7 @@ static FILE *out;
 
 static int line_comp(char *ex, char *in, int l)
 /*
-** Compare exclude line with inline
+** Compare exclude line with cinline
 */
 {
     return strncmp(ex,in+11,l);
@@ -28,13 +28,13 @@ static void process()
 */
 {
     char exline[MAXLINE];
-    char inline[MAXLINE];
+    char cinline[MAXLINE];
     char *exok, *inok;
     int compare;
 
 
     exok = fgets(exline,MAXLINE,ex);
-    inok = fgets(inline,MAXLINE,in);
+    inok = fgets(cinline,MAXLINE,in);
 
     while (exok && inok) {
 
@@ -43,15 +43,15 @@ static void process()
 	if (compare < 0)
 	    exok = fgets(exline,MAXLINE,ex);
 	else if (compare > 0) {
-	    fprintf(out,"%s",inline);
-	    inok = fgets(inline,MAXLINE,in);
+	    fprintf(out,"%s",cinline);
+	    inok = fgets(cinline,MAXLINE,in);
 	} else
-	    inok = fgets(inline,MAXLINE,in);
+	    inok = fgets(cinline,MAXLINE,in);
 
     }
 
-    while (inok = fgets(inline,MAXLINE,in))
-	fprintf(out,"%s",inline);
+    while (inok = fgets(cinline,MAXLINE,in))
+	fprintf(out,"%s",cinline);
 
 }
 

src/indexseqlibs/makefile-alpha

@@ -2,6 +2,7 @@
 # indexseqlibs - Alpha version
 #
 
+all: $(PROGS)
 
 #
 # Programs need making