Adding reference genomes to local instance of Galaxy using Rsync

Question: Adding reference genomes to local instance of Galaxy using Rsync

3.7 years ago by

gkuffel22 • 170

United States

gkuffel22 • 170 wrote:

Hi everyone,

We were finally successful in downloading selected reference genomes as they appear on the Main instance of Galaxy using Rsync. For example, we have successfully downloaded hg19 and it is located on our server in the Galaxy directory. The problem now is we do not know how to get these files to populate the drop-down menus and be available to respective tools. Can we use Data Managers? We have tried, however when we select to get the genome from our server using the correct path and run Data Managers it completes successfully but hg19 still does not appear to be available in the drop-downs for any of the tools. Does anyone know where we are going wrong?

galaxy rsync • 1.9k views

ADD COMMENT • link •

modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by gkuffel22 • 170

3.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are just getting reference genomes, you can obtain them directly from the source in most cases using the fetch genome Data managers. "hg19" came from UCSC. One DM is for when the builds list already contains a genome (by "dbkey") and one is for when you want to add a new genome.
https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_all_fasta

Then, to have the genome available in certain tools, indexes are needed. Definately create a 2bit file, Picard indexes, and SAMTools indexes (for almost any Galaxy, these are required basics for default functionality). Specific tools require specific indexes, for example Bowtie2/Tophat2 require Bowtie indexes. There are different Data Managers for different indexes. And new ones can be created as needed.

DMs in the Main tool shed should all work without issue. DMs in the Test Tool Shed may or may not be fully useable.
http://usegalaxy.org/toolshed
http://testtoolshed.g2.bx.psu.edu/

For reference, indexes and such can be managed manually as well. This may be a choice for certain tools. The set of wikis here can help (along with any tool's underlying documentation):
http://wiki.galaxyproject.org/Admin/DataIntegration
http://wiki.galaxyproject.org/ToolShed

Best, Jen, Galaxy team

ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »