I have installed the rsync data manger into galaxy and am attempting to locate the human genome assemblies through the dbkey search but no results are populating the field. Previously I was able to use this to find the genomes I needed but now it appears to no longer function. Is there a better method to adding genomes for use in a local galaxy other than this.
Hello,
We will follow up for the rsync fetching option problems (this has come up before, but is not ticketed). If you have time, could you add a comment about which genome - specifically by dbkey - is problematic?
Meanwhile, alternatives include:
Obtaining the data directly from rsync locally, loading it into a history, then using that as input. (Just get the <dbkey>/seq/<dbkey>.fa file). Once the new genome has been added, create all indexes new on your instance. It is only worth doing this for genomes that you find at http://usegalaxy.org but are not available at the original public source, or have been modified in some way to not be the same as the public source. There are very few of this type.
Load any fasta file into a history the admin account can access and run the data manager on the file that way. This is similar to item 1 above, but the source would not be the rsync server, but some other public data resource, or your own groups genome/transcriptome builds.
Load the data from the public source directly (when that source is supported by the fetching tool).
Not directly related, but has much information about reference genomes in general and how to avoid issues with them - for you and others reading later - (I am guessing that you chose to use rysnc originally to avoid a mismatch problem): https://wiki.galaxyproject.org/Support#Reference_genomes
Hope one of these works out for you, but let us know if not.
Jen, Galaxy team
Thank you. No specific genome is causing an issue; specifically when I search using db key in the Rsync data manager no results populate as they previously did.
I am searching for hg19 and grch37.
I just successfully used the rsync data manager (exact version) in a local based on Galaxy release 16.04. The database was hg19, but all of the other available data was there in the initial drop-down menu and associated tables with checkboxes.
If you have made other modifications to your local or you running Galaxy from the development branch, that could be the source of the problem.
Try updating your server to use the master 16.04 branch, uninstall the data manager, then reinstall it. Follow this by restarting your local instance. The problems should resolve, but let us know.
Thanks! Jen, Galaxy team
I tried on two separate instals with the same issue. These were both setup using the main branch and have the same issue of no dbkey working in the search bar.
When I tested, I did the very basics described at http://getgalaxy.org. Including the admin set up near the bottom the page. I only installed this tool.
If you do the same as a test (without other modifications) - does the tool work then?
We can follow up with more, but this is the simplest way to start. When you reply, please note if you are using a MAC or PC or some other type of server (specify OS, please). Also please note the python version Galaxy is using.
Thanks! Jen, Galaxy team
I installed a test on my CentOS server using only default parameters and the search function does work with R2. Galaxy is using python 2.7.
Ok, this narrows down the issue. Some change made to your other instances is causing the problem. The ways that an instance can be customized are vast. It may be quicker for you to replicate those changes in your working test instance, one (or a very few) at a time, and find out what the problematic trigger is. We would be interested in knowing the outcome to see if it can be addressed (corner-case bug with the tool or some type of incompatibility, etc).
Thanks! Jen
