Question: Error in integrating a local database in to galaxy
0
gravatar for sursngika
6 weeks ago by
sursngika0
sursngika0 wrote:

Hi,

I have a local instance of galaxy. I have created a database by locally downloading bacterial 16S from refseq database. inside db folder i have refseq, refseq.nhr, refseq.nin, refseq.nog, refseq.nsd, refseq.nsi, refseq.nsq files.

In blastdb.loc file inside galaxy tool-data folder, I have mede an entry as below.

refseq<tab>refseq 02 Oct 2017<tab>/home/sumudu/git/galaxy_infectious/galaxy-v1.0/db/refseq

And then pointed the .loc file in megablast.xml file in galaxy as below.

megablast_wrapper.py --db_build=$/home/sumudu/git/galaxy_infectious/galaxy-v1.0/tool-data/blastdb.loc

<test> <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> <param name="database" type="select" label="Nucleotide BLAST database"> </param> <param name="source_select" value="/home/sumudu/git/galaxy_infectious/galaxy-v1.0/tool-data/blastdb.loc"/>

But when run blast I get an error : Cannot locate the target database directory. Please check your location file.

Can someone please help me to figure out what went wrong.

Thank you

Rangi

ADD COMMENTlink modified 6 weeks ago by Jennifer Hillman Jackson23k • written 6 weeks ago by sursngika0
0
gravatar for Jennifer Hillman Jackson
6 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

You are pointing to a specific database instead of a choice (based on the .loc) as a source for the reference database (and associated indexes). The tool is not designed that way. The original .xml section that points to a select list input should be used (loc content is implied but not specifically included in that area of the wrapper).

If you want to restrict the usage to a specific database, only include that in the .loc. Or if many databases will be present but you are trying to build up a process others can use to follow a specific processing path - put all of it into a workflow with the target dataset option for megablast selected/set.

After making changes, restart Galaxy. Some reference data does update now without a restart but I am not sure if blast was included in that or not. Or try without restarting and if have problems, then restart to reset the content.

There isn't an existing Galaxy mapping tool that I can think of that points to a single specific database instead of a select list - so cannot give you an example to model after if you really want/need to modify the megablast wrapper to only have one default database as the target. But I can let you know this would involve more than changing that single line in the xml and the loc wouldn't be used/invoked. Changes would be to the .xml data handling, tool form itself (current has a select list for database), and probably the .py as well.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Jennifer Hillman Jackson23k

Hi Jen,

Thank you very much for the answer. Its true and even if I tried changing .xml files it didn't work. But managed another way.

I added ncbi_blast_plus tool package from tools shed. changed its blastsb.loc file to point to my local database. And set the local database path in galaxy/databases/dependancies/.........../ncbi_blast_plus/....../env.sh file. And it worked.

Best Regards Rangi

ADD REPLYlink written 6 weeks ago by sursngika0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 129 users visited in the last hour