Question: Error in integrating a local database in to galaxy
0
gravatar for sumudu_rangika
2.6 years ago by
sumudu_rangika30 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

galaxy megablst blastdb.loc • 786 views
ADD COMMENTlink modified 2.6 years ago by e.rempel810 • written 2.6 years ago by sumudu_rangika30

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

ADD REPLYlink written 2.6 years ago by genomax83k

Thank you. will do that.

ADD REPLYlink written 2.6 years ago by sumudu_rangika30
0
gravatar for e.rempel
2.6 years ago by
e.rempel810
Germany, Heidelberg, COS
e.rempel810 wrote:

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.

ADD COMMENTlink written 2.6 years ago by e.rempel810

Thank you will try that.

ADD REPLYlink written 2.6 years ago by sumudu_rangika30
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