Installing MAST from the MEME package

Evert-Jan Blom e.j.blom at biol.rug.nl
Thu Jul 10 20:52:34 EST 2003


Hello!

Recently I've installed and tested the Meme/Mast package. The MEME package
works flawlessly, giving us some nice results.
The MAST package however doesn't function properly.

After filling in the mail field in the
/meme/website/cgi-bin/process_request.cgi  site
(the motif field was already filled since we used the link from a Meme mail)
and using Bacillus subtilis as the sequence database option.

(We made a MAST DB folder and a symbolic link and filled it with files from
the NCBI)

After pressing search we encountered the following message:

Error Report:
1. while: Missing file name.
There was 1 error on the form. Please correct it and try again.

We checked the MAST.cgi file and we suspect the following passage to be
creating the error message:

print "thisisshown";
# convert the meme file to log-odds format and get the sequence alphabet
$lo_file = "mast.logodds.$$";
if ($motifs_found) {
$_ = `csh $bin/make_logodds $motif_file $lo_file -D $gawkdir 2>&1`;
# check that conversion succeeded
@words = split();
$size = @words;
if ($size >= 1 && $size <= 2) {
$alphabet = $words[0];
} else {
&whine("@words");
$motifs_found = 0;
}
}

Thanks in advance

Evert-Jan Blom
Department of Molecular Genetics
Holland






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