LOLAweb

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i'm seeing that the pre-loaded region set for mm10 is empty ... as is universe select list for mm9

there's nothing in the example folder for mm10, you're right...

but the universe for mm9 is populated.

I've added an example dataset now to the mm10 folder.

I'm not sure why it's not now showing up in the app, though.

@nmagee Does the container need to be rebooted (to allow the volume to be remounted) or something before it will show up in the app?

it doesn't seem like it should...

@vpnagraj is this possibly caused by the app loading up the file list too early?

Anything we drop into an already-mounted Qumulo share should be immediately visible to the container, no rebuild or reboot needed.

That's what I thought... but this file is there:

ls $LWREF/examples/mm10/
SE_bone_marrow.bed

but doesn't show up under mm10 on the actual app...

Interesting. I hopped into a production LOLAweb container, changed to that dir, and see nothing:

root@fab10143a65f:/mnt/q/shefflab/LOLAweb/examples/mm10# ls -al total 8 drwxrwxr-x 2 854360 25014 0 Apr 13 2018 . drwxrwxr-x 6 854360 25014 3584 Apr 19 16:54 ..

But if I’m in Rivanna and follow that path, there it is.

I’m going to kill a container and hop into it and see what I can find.

Okay, yes -- the .bed file is visible in a newly-spawned container. So I just re-launched all LOLAweb production containers.

Let me see if Docker explains this better than I can, but as I now recall any externally mounted volume isn't truly a pass-through (internal-external) like we think of a regular NFS mount. It's actually a cached copy of the dir within the container, and Docker takes care of writing out to the share when new files are created. Unless there is some permissions issue I don't know of, it doesn't bring a "new" external file into the cached volume automatically.

Or I may have mounted these in a simpler, more naive way than we need. I'll research and try to make this more seamless so you can add files as you like.

https://stackoverflow.com/questions/45282608/how-to-directly-mount-nfs-share-volume-in-container-using-docker-compose-v3

FWIW i can confirm that i'm seeing the mm10 example file now too ... and was able to execute a run with it