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databio / LOLAweb

An interactive Shiny web application for genomic interval enrichment analysis using LOLA.
http://lolaweb.databio.org/
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examples should auto-populate their reference genomes #76

Closed nsheff closed 6 years ago

nsheff commented 6 years ago

we can't run an hg19 sample on an mm10 database.

2 solutions: when you choose a sample, it populates the appropriate genome; or when you pick a genome, it restricts the dropdown to samples for that genome.

I've started to implement these but reached my limit as I don't know how to find the input variable. @vpnagraj ?

vpnagraj commented 6 years ago

i started on this went with option two:

when you pick a genome, it restricts the dropdown to samples for that genome

that seems to be working (in the sense that i can see the 2 bed files in hg19/ when i select hg19) ... but when i try to run a job i'm getting an error

@nsheff can you double check the permissions on those example files? maybe similar to what we were seeing in #50 yesterday?

also wondering if we will have example usersets for all of the reference genomes?

nsheff commented 6 years ago

Yep, permissions fixed it. That is great, thanks. This works.

I'll make sure to add examples for all of the reference genomes.

vpnagraj commented 6 years ago

@nsheff have you successfully completed a run with either of the example user sets?

i see that they load and start processing but i get disconnected at the end (when the cache is being created)

maybe also related to discussion in #50 and how the cache dir is being mounted on containers? is shiny not able to write to that location?

nsheff commented 6 years ago

yes, they are working for me.

I just depends on if you got a container that's correctly mounting cache. it's exactly #50, looks like you're assigned to the bad containers now and I got the good ones.