Question: Custom Blast Db On Galaxy Server
4
gravatar for Zach Powers
7.2 years ago by
Zach Powers340
Zach Powers340 wrote:

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

galaxy • 4.2k views
ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Zach Powers340
2
gravatar for Zach Powers
7.2 years ago by
Zach Powers340
Zach Powers340 wrote:

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
ADD COMMENTlink written 7.2 years ago by Zach Powers340

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.

ADD REPLYlink written 7.2 years ago by ALchEmiXt1.9k

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.

ADD REPLYlink written 7.2 years ago by ALchEmiXt1.9k

thanks alchemixt

ADD REPLYlink written 7.2 years ago by Zach Powers340

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?

ADD REPLYlink written 3 months ago by feliyon860
1
gravatar for Pawel Szczesny
7.2 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Pawel Szczesny3.2k
0
gravatar for Vitis
7.2 years ago by
Vitis1.9k
New York
Vitis1.9k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Vitis1.9k

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.

ADD REPLYlink written 7.2 years ago by Zach Powers340
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