Question: Adding reference genomes to local instance of Galaxy using Rsync
gravatar for gkuffel22
3.7 years ago by
United States
gkuffel22170 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 COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by gkuffel22170
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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.

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.

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):

Best, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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