--- args.cpp.new	2006-06-15 15:09:53.000000000 +0200
+++ args.cpp	2006-06-15 15:10:11.000000000 +0200
@@ -5,7 +5,6 @@
 
 #include <ostream>
 #include <unistd.h>  // getopt
-#include <stdlib.h> // getenv
 #include "MCFgen.hpp"  // die, tostring
 #include "MCFbio.hpp"  // count_residues
 #include "args.hpp"
@@ -58,7 +57,7 @@
 of sequence motifs in a FASTA-like format described below. Any non-alphabetic\n\
 characters in the sequences are ignored, and any alphabetic characters except A,\n\
 C, G, T (uppercase or lowercase) are converted to 'n' and excluded from matching\n\
-motifs. The motif file, specified either in the CLOVER_MOTIF_FILE variable or as clover option, should look like this:\n\
+motifs. The motif file should look like this:\n\
 \n\
 >TATA\n\
 0 0 0 10\n\
@@ -130,7 +129,6 @@
 In addition to the two required inputs, there several options for modifying\n\
 Clover's behavior:\n\
  -h  Help: print documentation. You already know this one.\n\
- -f  alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n\
  -r  Number of randomized/control raw scores to calculate for comparison with\n\
      each target raw score.\n\
  -t  P-value threshold: only print results for motifs whose P-values don't\n\
@@ -162,12 +160,9 @@
 ";
 
   const string usage =
-    "Usage summary: clover [options] myseqs.fa [BGfiles]\n"
-    "\nYou should set the CLOVER_MOTIF_FILE environmental variable\n"
-    "or specify the path to a motif file as clover option\n\n"
+    "Usage summary: clover [options] mymotifs myseqs.fa [BGfiles]\n"
     "Options:\n"
     "-h  help: print documentation\n"
-    "-f  alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n"
     "-r  number of randomizations (" + tostring(shuffles) + ")\n"
     "-t  P-value threshold (" + tostring(pthresh) + ")\n"
     "-u  motif score threshold (" + tostring(hit_thresh) + ")\n"
@@ -180,20 +175,13 @@
     "-s  seed for random number generator (" + tostring(random_seed) + ")\n"
     ;
 
-  char *cptr;
-  if ((cptr = getenv( "CLOVER_MOTIF_FILE" )) != NULL ) {
-     mat_file = cptr;
-  }
   int c;
 
-  while ((c = getopt(argc, argv, "hf:r:t:u:ndmlvp:s:")) != -1)
+  while ((c = getopt(argc, argv, "hr:t:u:ndmlvp:s:")) != -1)
     switch (c) {
     case 'h':
       cout << doc << endl;
       exit(0);
-    case 'f':
-      	mat_file = optarg;
-	break;
     case 'r':
       shuffles = atoi(optarg);
       break;
@@ -228,12 +216,10 @@
       mcf::die("\n" + usage);  // "invalid option" message is printed by getopt
     }
 
-  if (mat_file.empty())
-    mcf::die("*** Error: Motif file not specified\n\n" + usage);
-
-  if (optind + 1 > argc)  // there should be 2 more non-option arguments
-    mcf::die("*** Error: sequence file required\n\n" + usage);
+  if (optind + 2 > argc)  // there should be 2 more non-option arguments
+    mcf::die("Error: motif and sequence files required\n\n" + usage);
 
+  mat_file = argv[optind++];
   seq_file = argv[optind++];
 
   while (optind < argc)