Thank you will try that.
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sumudu_rangika •
Error in integrating a local database in to galaxy
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=$/home/sumudu/git/galaxy_infectious/galaxy-v1.0/tool-data/blastdb.loc*
<test>
<param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
<param name="database" type="select" label="Nucleotide BLAST database">
</param>
<param name="source_select" value="/home/sumudu/git/galaxy_infectious/galaxy-v1.0/tool-data/blastdb.loc"/>
But when run blast I get an error : Cannot locate the target database directory. Please check your location file.
Can someone please help me to figure out what went wrong. Thank you Rangi
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e.rempel
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sumudu_rangika •
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sumudu_rangika •
1 answer
Hi Rangi,
I have a small suggestion, but otherwise, you could post your question on this forum.
I think you should remove the dollar sign in megablast_wrapper.py *--db_build=$/home/sumudu/, because it looks like an absolute path to blast database.
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Please post this over at the Galaxy biostars site for quicker resolution.
Thank you. will do that.