Error in integrating a local database in to galaxy

Question

[sumudu_rangika]

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

[GenoMax]

Please post this over at the Galaxy biostars site for quicker resolution.

[sumudu_rangika]

Thank you. will do that.

Answer 1

[e.rempel]

Hi Rangi,

I have a small suggestion, but otherwise, you could post your question on this forum.

I think you should remove the dollar sign in megablast_wrapper.py *--db_build=$/home/sumudu/, because it looks like an absolute path to blast database.

[sumudu_rangika]

Thank you will try that.