[EMBOSS] copying emboss indexes to another directory

[Jon Ison]

Dear Alexis


Typically index files are kept in the same directory as the database itself.
It is ok to move the index & database files (no need to regenerate the
indices)
so long as you reconfigure the database by updating the database
declaration in
your configuration files*.

Use 'showdb' to get a list of valid database names currently set up.

The maintenance of your config files is easier if you specify the location of
your databases as an environment variable. Then if you move things you
only need
to update one line:

set emboss_database_dir /data/databases/flatfiles

This would then be referred to later in .embossrc as

\$emboss_database_dir/embl

for the directory /data/databases/flatfiles/embl


If that doesn't help please get back in touch.

Cheers

Jon


* emboss.default (share/EMBOSS subdirectory of your installation) or
.embossrc
files (in the directory specified by the EMBOSSRC environment variable / your
home directory / current directory).

See the admin guide:
http://emboss.sourceforge.net/docs/adminguide/node4.html



>
> Hello
>
> I would like to know if there is any problem if I copy my emboss index
> files to another directory and then define another database description
> in the emboss.default configuration file.
> I have been moving files from our current disk to another with more
> room, will it be necessary to regenerate the indexes again with dbiflat?
>
>
>
>
> Some error messages :
>
> seqret UniProtRebost:108_LYCES
> Reads and writes (returns) sequences
> Error: Cannot open database file 'uniprot_sprot.dat'
> Error: Unable to read sequence 'UniProtRebost:108_LYCES'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
>
> ## UniProtRebost is the definition for our UniProt at the new disk.
>
> Done some debugging to seqret with -debug option. It seemed seqret was
> searching for uniprot_sprot.dat at the same directory in the new disk
> where I copied the indexes I had on the old disk.
>
>
>     A lot of thanks!
>
>
>     Alexis.
>
>
> -----------------------------------------------------
> Alexis Torrano Martinez
> e-mail: atorrano at lsi.upc.edu
>
> Nodo Computacional GNHC-2 UPC-CIRI (inb.lsi.upc.edu)
> Instituto Nacional de Bioinformatica (www.inab.org)
> Barcelona Supercomputing Center Node (www.bsc.es)
>
> c/. Jordi Girona 29
> Edifici Nexus II, despatx 113  Tel:  (+34) 93 413 4037
> E-08034 Barcelona              Fax:  (+34) 93 401 7055
> Catalunya (Spain)
> Team info:
> http://www.inab.org/~malaga/MOWServ/services/HELP/MarcoBajo/team.html
> -----------------------------------------------------
>
>
>
>
>
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at emboss.open-bio.org
> http://newportal.open-bio.org/mailman/listinfo/emboss
>