Hi Kenneth,

Yes, target databases require indexes and *.loc file set-up. Please see this wiki for details. For Genbank data such as NR, FTP the pre-built indexes and use those (generating them with formatdb is not necessary).


http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

See the second section, 'Tips for Installing Tools -> 'Megablast installation', then down in the wiki again under 'Megablast' for more detail. The same indexes can be used for BLAST+ (both now are based on BLAST+). The location of the data can be where you have it - it seems like Galaxy is looking in the right place for it (it does not go under a genome like the other indexes on the wiki).

Also, make sure the data is uncompressed before you use it. And be sure to point to the data into the blastdb.loc file (this appears to be done already based on your error message, but double check).

Hopefully this helps,

Jen
Galaxy team

On 9/17/12 10:11 AM, Kenneth R. Auerbach wrote:
Hi Jennifer,

Thank you for that info. I have another question, when I submit my job I
get this error:

-----
An error occurred running this job: BLAST Database error: No alias or
index file found for protein database
[/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search
path
[/9720/galaxyprod/galaxy-dist/database/job_working_directory/1560::]
Return error code 2 from command:
blast
------
I checked and the 'nr' database file is there in that path and it has
read permissions for everyone.  It's in a directory called 'nr-newstyle'
with only its archive file (.gz). There are no other files. Should there
also be 'alias' or 'index' files as well? Are other files needed besides
'nr'?

Thank you.

On Mon, 2012-09-17 at 09:29 -0700, Jennifer Jackson wrote:
Hello Kenneth,

Are you using BLAST+ in a local install or cloud instance? The problem
may be that the query dataset needs to have the datatype assigned as
"fasta". To do this, click on the pencil icon for the dataset to reach
the Edit Attributes form. Then either scroll down to (or click on the
tab for) the attribute "Datatype" and change to "fasta" and save. [The
UI is undergoing some changes, so you may or may not have the new tabs
style form in your instance yet).

The best mailing list going forward for local/cloud support is
galaxy-...@bx.psu.edu.
http://wiki.g2.bx.psu.edu/Mailing%20Lists

Take care and please let us know if your question has been misunderstood,

Jen
Galaxy team

On 9/17/12 8:52 AM, Kenneth R. Auerbach wrote:
Hello,

I'm new to Galaxy.
When I read in a fasta file to Galaxy and then try to use it (in a blast
search) as the query sequence, I get the error message below, although
the uploaded fasta file is present in the history.  Can anyone tell me
what the problem could be? Is there some other step I need to do?

Thank you.

Error that appears under "nucleotide query sequence":
-----
"History does not include a dataset of the required format / build"
-----

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

    http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

    http://lists.bx.psu.edu/





--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to