$NetBSD: patch-aa,v 1.2 2005/11/03 19:52:44 rillig Exp $

--- test/testxylem.csh.orig	2001-08-18 16:31:51.000000000 -0400
+++ test/testxylem.csh	2003-09-28 17:29:21.000000000 -0400
@@ -10,13 +10,12 @@
 # set default parameters
 #####################################################################
 set RM = rm
-set BINDIR = ../bin
 
 # set $testset to programs to be tested.
 set NUMARGS = $#argv
 
 if ($NUMARGS == 0) then 
-   set TESTSET = (splitdb getloc identify getob reform ribosome shuffle\
+   set TESTSET = (splitdb getloc xyl-identify getob reform ribosome shuffle\
                   dbstat flat2phyl findkey fetch features)
 else
    set TESTSET = $1
@@ -31,7 +30,7 @@
     ######### splitdb #######
     case splitdb:
        # run the program
-       $BINDIR/splitdb sample.gen temp.ano temp.wrp temp.ind
+       splitdb sample.gen temp.ano temp.wrp temp.ind
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -73,7 +72,7 @@
     ######### getloc #######
     case getloc:
        # run the program
-       $BINDIR/getloc sample.nam sample.ano sample.wrp sample.ind temp.gen
+       getloc sample.nam sample.ano sample.wrp sample.ind temp.gen
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -95,10 +94,10 @@
       breaksw
 
     ######### identify #######
-    case identify:
+    case xyl-identify:
        # run the program
        egrep -n -i LOCUS sample.ano >temp.egrep
-       $BINDIR/identify temp.egrep sample.ind temp.nam temp.fnd
+       xyl-identify temp.egrep sample.ind temp.nam temp.fnd
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -132,7 +131,7 @@
     ######### getob #######
     case getob:
        # run the program
-       $BINDIR/getob sample.inp sample.nam sample.ano sample.wrp sample.ind\
+       getob sample.inp sample.nam sample.ano sample.wrp sample.ind\
                      temp.getob.msg temp.getob.out temp.getob.exp
 
        # if successful, compare sample files with new output
@@ -175,7 +174,7 @@
     ######### reform #######
     case reform:
        # run the program
-       $BINDIR/reform -g -p -c -fi <sample.aln > temp.ref
+       reform -g -p -c -fi <sample.aln > temp.ref
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -199,7 +198,7 @@
     ######### ribosome #######
     case ribosome:
        # run the program
-       $BINDIR/ribosome <sample.out > temp.pep
+       ribosome <sample.out > temp.pep
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -223,7 +222,7 @@
     ######### prot2nuc #######
     case prot2nuc:
        # run the program
-       $BINDIR/prot2nuc <sample.pro > temp.prot2nuc
+       prot2nuc <sample.pro > temp.prot2nuc
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -247,7 +246,7 @@
      ######### dbstat #######
     case dbstat:
        # run the program
-       $BINDIR/dbstat <sample.pep > temp.dbstat
+       dbstat <sample.pep > temp.dbstat
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -272,7 +271,7 @@
     case flat2phyl:
       
        # check results for interleaved format
-       $BINDIR/flat2phyl <sample.flat > temp.interleaved.phylip
+       flat2phyl <sample.flat > temp.interleaved.phylip
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -295,7 +294,7 @@
        endif
 
        # check results for sequential format
-       $BINDIR/flat2phyl -s <sample.flat > temp.sequential.phylip
+       flat2phyl -s <sample.flat > temp.sequential.phylip
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -321,7 +320,7 @@
    ######### shuffle #######
     case shuffle:
        # run the program
-       $BINDIR/shuffle -s3456 <sample.out > temp.shuf
+       shuffle -s3456 <sample.out > temp.shuf
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -337,7 +336,7 @@
     case findkey:
        # run the program
        echo "LOCUS" > temp.kw
-       $BINDIR/findkey -G sample.ano temp.kw temp.nam temp.fnd
+       findkey -G sample.ano temp.kw temp.nam temp.fnd
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -371,7 +370,7 @@
     ######### fetch #######
     case fetch:
        # run the program
-       $BINDIR/fetch -G sample sample.nam temp.gen
+       fetch -G sample sample.nam temp.gen
 
        # if successful, compare sample files with new output
        set SUCCESS = $status
@@ -396,7 +395,7 @@
     case features:
        # run the program
        cp sample.exp temp.exp
-       $BINDIR/features -u sample -E temp.exp 
+       features -u sample -E temp.exp 
 
        # if successful, compare sample files with new output
        set SUCCESS = $status