Question: Installing Databases for MegaBlast
1
gravatar for Dale.Kunde
3.5 years ago by
Dale.Kunde10
Australia
Dale.Kunde10 wrote:

Hi all

I am currently running a GVL image of galaxy on a Nectar Cloud Server. The native system works well. I am trying to install some tools to customise the image and those tools that install with dependencies already a part of the image work fine. I am trying to install the MegaBlast tools and have installed the megablast_wrapper, package_blast_plus_2_2_26 and package_bx_python_0_7 from the toolshed. It appears all installed fine and is ready to go.

My question is how to (or into which directory) install the databases (eg wgs, nr). The megablast xml wrapper contains the line dbbuild="${source.select.fields.path}. Is this the line that points the tool to the databases? How would I change the line to direct it to a specific database? Would I download the databases from ncbi, upload them to a folder and then point this line to the folder?

Any help in finding the solution would be greatly appreciated.

Dale

databases galaxy megablast • 1.6k views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson23k • written 3.5 years ago by Dale.Kunde10
1
gravatar for fubar
3.5 years ago by
fubar1.1k
Australia
fubar1.1k wrote:

Hi, Dale. 

The tool xml includes a datatable reference:

<param name="source_select" type="select" display="radio" label="against target database">
            <options from_data_table="blastdb" />
</param>

That means it will look at the blastdb.loc table for genome options and file paths. Setting these up locally is a bit of a black art involving editing the .loc file to point to freshly downloaded genomes and indexes in specific paths, but is documented in the .loc file itself and in various places in the wiki - eg https://wiki.galaxyproject.org/Admin/DataPreparation?action=show&redirect=Admin%2FNGS+Local+Setup mentions megablast under Tools and Their Corresponding loc Files

I hope this helps - I'm sure the GVL support team can also provide more specific advice.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by fubar1.1k

Thanks Ross. I'm still working out the galaxy file structure and processes in my head so this is very helpful. Dale

ADD REPLYlink written 3.5 years ago by Dale.Kunde10
0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello Dale,

If you want to see the exact commands/paths that are used for the http://usegalaxy.org set up for Megablast indexes (mirror what is in the wiki, but include command-lines, etc), there are README files available from our rsync server.

How to:
https://wiki.galaxyproject.org/Admin/UseGalaxyRsync

The files of interest are:
blastdb/README
blastdb/log/2014_README_LOG

There are also some very simple test data/commands available in the dir:
blastdb/test

If setting up the phylogenetic tools, then you will also want to take a look at the contents of:
taxonomy

Maybe will help? Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 114 users visited in the last hour