Custom Blast Db On Galaxy Server

Question

[Zach Powers]

Hello Biostar,

I have recently set up a Galaxy server for my group as we are interested in setting up workflows for common bioinformatics tasks. So far so good - things are up and running but I've run into my first issue: how can I customize Blast? Right now I can blast one fasta file against another but I would like to make Galaxy aware of a number of custom Blast Databases that we have so that a user could blast their fasta file against them using only a pulldown menu.

While i have found Galaxy to be very promising I can't find too much info on customizing the tools. Any help would be greatly appreciated!

thanks zach cp

Answer 1

[Zach Powers]

Got it! In the Galaxy home directory */galaxy-dist is the /tool-data/ folder which contains the blastdb.loc file. The information on how to specify blast databases is contained in the file but basically you just modify this file to make Galaxy aware of where your Blast Databases are. In our case I will add entries for the common NCBI-mirrored sequecnes as well as our custom databases. Example from the file header below:

Your blastdb.loc file should include an entry per line for each "base name" 
you have stored.  For example:

nt_02_Dec_2009      nt 02 Dec 2009      /depot/data2/galaxy/blastdb/nt/nt.chunk
wgs_30_Nov_2009     wgs 30 Nov 2009     /depot/data2/galaxy/blastdb/wgs/wgs.chunk

[ALchEmiXt]

Do not forget the reboot the galaxy instance to make the galaxy server aware of the new BLAST databases. Similarly, this loc file configuration also works the same for preconfigures bowtie and bwa indexes.

[ALchEmiXt]

Do not forget the reboot the galaxy instance to make the galaxy server aware of the new BLAST databases. Similarly, this loc file configuration also works the same for preconfigures bowtie and bwa indexes. Thus far there is no option to add datasets in realtime to loc file preconfigured sets.

[Zach Powers]

thanks alchemixt

[feliyon86]

Hello,

I have similar problem, but since this post is old, I don't know if it has changed. I am using only one single version.

nt NCBI nt (partially non-redundant) Mar.2017 home/galaxy/ncbi_db/nt/nt

I tried with chunk or not in the blastdb.loc but not successful, recommendations?

Answer 2

[Pawel Szczesny]

It is possible (or was, as I did it some time ago and don't have access to that installation anymore) using .loc files. See this guide http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup - there's some info on Megablast customization.

However I agree that Galaxy documentation is a bit lacking in administrative areas.

Answer 3

[Vitis]

I don't have a Galaxy solution for this, I use wwwblast package for this purpose, it's quite outdated now but still serves. You can have any number of databases showing up in a pulldown menu.

[Zach Powers]

thanks vitis, but I need this to fit into a Galaxy workflow. We can use command line for blasting but I am hoping the Galaxy tools will let us reproduce/automate our queries.