Some help required.
peter.rice at uk.lionbioscience.com
Tue Jul 30 11:00:06 EDT 2002
Alex Brown wrote:
> In order to get the 'showdb' command to list the available databases, I
> uncommented the first line of the emboss.default.template file (SET
> emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to
> emboss.default. The command 'showdb' results in the following output:
> indicating the databases in the /local/share/EMBOSS/test directory.
> So far so good.
> However, attempting to work through the tutorial on the EMBOSS web-site,
> I find that I am unable to access the databases: for example
> [xxxxxx:~] me% seqret
> Reads and writes (returns) sequences
> Input sequence(s): tembl:hs*
> Warning: Cannot open division file '<null>'
> Warning: seqCdQry failed
> Error: Unable to read sequence 'tembl:hs*'
> Input sequence(s):
First, I assume your emboss.default file has:
SET emboss_tempdata /local/share/EMBOSS/test
Next, you can try:
This will write a file seqret.dbg where I would expect lines like this:
directory '/local/share/EMBOSS/test/embl' entry 'hs*' acc 'hs*'
ajNamResolve of '/local/share/EMBOSStest/embl/division.lkp'
This is the division file which it says cannot be opened.
If you see what appears to be the right filename, check file (and
If you see something else, it may give a clue to where the setup is wrong,
or you can get help from emboss-bug at embnet.org
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723
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