Question: Getting ftp link to file on galaxy ftp server in order to share or feed to IGV
0
gravatar for prishly
14 days ago by
prishly0
prishly0 wrote:

Hi!

Is there any way I could get a direct url to my files that I have uploaded to galaxy ftp-server so that I could share them with other users (at least with users registered on galaxy) or paste the link to feed files into IGV?

I got this idea from this post https://biostar.usegalaxy.org/p/3084/

UPDATE: I've just been told one way could be copying link when uploading to Galaxy ftp-server with FileZilla (the link is available through FZ interface)... but it didn't work when I tried to use the ftp-link to the file uploaded by a friend

ftp url igv galaxy file sharing • 91 views
ADD COMMENTlink modified 13 days ago by Jennifer Hillman Jackson25k • written 14 days ago by prishly0
0
gravatar for Jennifer Hillman Jackson
13 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The post you reference is 7+ years old, and both Galaxy and IGV have evolved since then.

The Galaxy FTP holding area is for intermediate data transfer purposes only. Any data loaded there will remain for three days or until moved into a Galaxy history. It is not intended to be a data hosting service for 3rd party applications. You should first move the data into a history (at a public Galaxy server) or data library (admin function only) in order to share it with others.

Datasets completely loaded into Galaxy (FTP followed by Upload to move the data into a history) will each have a disc icon. That can be shift-clicked on to copy the URL. Others can copy the data using the URL(s). It can be downloaded locally (curl, wget), pasted back into the Upload tool (to create a copy into their Galaxy account, even if at a different Galaxy server), or used externally.

Few more details:

  • IGV is available as a direct resource link for datasets within Galaxy (if the datatype is supported by IGV).
  • Local IGV by default will be available per dataset via a link within the dataset. Download IGV, set up start the application, load a custom genome or one of those indexed in the IGV resource bundle into your IGV, and assign the database (if not assigned during Upload or by a tool already). A local IGV should be launched, running, and have the same genome prepped/loaded before using the Galaxy link.
  • The database (genome name/dbkey) must be the same between Galaxy and IGV. This may involve promoting a custom genome to a custom build within Galaxy. Custom builds can be assigned as a "database" metadata attribute -- at Upload (in batch, faster) or after (per dataset).
  • Public IGV will be available as a per-dataset resource link as well IF the database matches what they host (a few common genomes, example: hg38).
  • The entire history containing the data can be shared with others by using a Share link (History menu > Share or Publish). Others can import it and access the individual dataset URL links themselves.
  • The data can be put into a dataset collection for batch download or for loading back into Galaxy (collections also have a disc icon/URL). The dataset collection data will be in a .tgz archive if downloaded. I'm not sure if IGV will load collection data directly by URL in batch or not -- you'll need to test it if this interests you (I will too, am curious). If it doesn't, then any downloaded archive will need to be unpacked to access the individual datasets within it (outside of Galaxy). Downloaded histories also can be unpacked to access the individual datasets.
  • If you are running your own Galaxy (as an admin) and it is publically hosted online, the data could be moved from a history into a Data Library, or often better, directly loaded into a data library. Data in data libraries are persistent the same as data in a history (unless actively deleted) and can be directly imported when using the same server without actually duplicating the data (data does not count toward user quota). Or it can be downloaded/transferred by URL. These datasets have a URL that can be used the same way that URLs from a history-dataset can be. The only difference is to capture the URL link from the dataset name as there won't be a disc icon in this view.

If you need help with any of the above, let us know which part, and we can send you doc/FAQ/Tutorial instructions. In most cases, downloading the data should not be needed to use it with 3rd party applications, a Galaxy history or library can host the data for URL sharing/loading.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 13 days ago • written 13 days ago by Jennifer Hillman Jackson25k
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