Move local repo to gannet

[yaaminiv]

In this issue @kubu4 pointed out that hummingbird was out of storage. He suggested I move my local project-virginica-oa to gannet, and work from my repo there.

I could easily clone my repo from the web onto gannet, but what about all of the large files from my local repo that are in my .gitignore? Is there an easy way to move those over besides just copying over files listed in my .gitignore?

[sr320]

I would use rsync..

[sr320]

Though maybe we should chat about why you might have a repo that is so large.

[yaaminiv]

My repo is large because I've performed multiple bismark runs on the full extent of C. virginica samples, which generated lots of large .bam files.

[sr320]

That should be done on Mox On Oct 10, 2018, 10:26 AM -0700, Yaamini Venkataraman notifications@github.com, wrote:

My repo is large because I've performed multiple bismark runs on the full extent of C. virginica samples, which generated lots of large .bam files. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[yaaminiv]

Yes, I will run bismark on Mox in the future. However, I'd like to use RStudio on hummingbird to test different methylKit parameters while bismark is running on Mox. Seeing how there is limited storage on hummingbird because of all of the large files in my repo, I was trying to free up some of the machine's storage while I continued to use it.

[sr320]

I think you have separate issues re large files and repos. Lets discuss IRL.

[kubu4]

Lets discuss IRL.

Good topic for lab meeting?

[yaaminiv]

Good topic for lab meeting?

@kubu4 Just what I was thinking

[yaaminiv]

@sr320 suggested I move all of the large files I generate in my repo to gannet (they wouldn't make it on Github anyways, so why keep them in a repo). I successfully mounted gannet on hummingbird, but do not appear to have write-access in the spartina folder.

I looked at the Data Management wiki which suggests navigating to gannet.fish.washington.edu and uploading files. When I do that, I get this screen:

TL;DR both methods of adding files to my gannet folder do not work.

[yaaminiv]

Edit: I think I just need my privileges updated. I was able to access File Station by going to https://128.95.149.52:5001

[kubu4]

I looked at the Data Management wiki which suggests navigating to gannet.fish.washington.edu

Thanks for heads up on this. Will fix (either set up redirect or change wiki to add port number to end of URL).

I've updated your permissions. Sorry about that. Something weird was going on. You were, correctly, listed as the owner of the folder, but for some reason didn't have Write permissions.

[sr320]

I updated index.html so wiki should be good

thanks Steven

Steven B. Roberts Kenneth K. Chew Endowed Professor School of Aquatic and Fishery Sciences University of Washington, Seattle WA sr320@uw.edu - 206.866.5141 robertslab.info - @sr320 On Oct 10, 2018, 1:23 PM -0700, kubu4 notifications@github.com, wrote:

I looked at the Data Management wiki which suggests navigating to gannet.fish.washington.edu Thanks for heads up on this. Will fix (either set up redirect or change wiki to add port number to end of URL). I've updated your permissions. Sorry about that. Something weird was going on. You were, correctly, listed as the owner of the folder, but for some reason didn't have Write permissions. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.