Unable to determine location of rsync data for all_fasta (human b38)

5

Hi @wdtraughber

How long it takes for corrections can vary. This one is still pending, and there isn’t an ETA yet.

I asked for an update directly on PR (pull request) here: https://github.com/galaxyproject/tools-iuc/pull/2839. You could do the same for any future fixes you may be tracking or waiting for.

Once the tool is updated, the PR will close out and you’ll find version 0.0.4 in the ToolShed (as @dave noted). The repository is here https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_rsync_g2/e0329ab30f6d. This is the same repository as browsed from within your server when installing tools as an admin.

Corrections/enhancement/updates lifecycle:

  1. Problem identified. An issue ticket may be created along with a PR or in some cases just an issue ticket (no PR yet), or just a PR (more common for technical fixes). This particular problem is tracked here at Galaxy Help, has an open PR, and had an issue ticket (linked to the PR).
  2. Fix is made. PR will close out first, then any associated issue tickets will close out.
  3. Fix applied. If the fix needs to be applied to a public server or resource that the issue ticket/PR is referencing, that is an extra step. When you are the admin pulling in a fix, the fix is for you to apply to your server. This could mean re-installing a tool or updating your server to capture a code update.

As an open-source project, we welcome and rely on community help and contributions! If you are interested in getting involved, please see: https://galaxyproject.org/develop/

If you are ever not sure about the status of a change, you can either review the issue/PR to check the status, update/test yourself, or ask for an update (on the issue ticket or PR is usually best for technical corrections). For this case, what you are watching for is the updated Data Manger, at the specified version, to become available in the ToolShed. But you could also follow or comment on the PR at Github to get notified with an alert when it closes out, changes state, has new comments, etc.

If you are in a hurry or just don’t want to wait: The Human GRCh38 genome sourced from UCSC (hg38) doesn’t need to be sourced from the Rsync server. That is just one choice. You could also install the same exact genome directly from UCSC using different Data Managers. This prior Q&A explains how: Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

Thanks!