Colin Diesh

Hi @nanjiangshu I know it's unfortunate but there are indeed a number of security alerts on the Apollo codebase right now that are reported by security scanners. I reported a...

certainly, let us know of any questions. there is some possibility the shiro could be upgraded to some patch version if that is the only one you need. see here...

i'm not sure what exactly shiro 1.2.5 is, i see only "1.2.1" here but not sure if we even use that https://repo.grails.org/ui/packages/gav:%2F%2Forg.grails.plugins:shiro?name=shiro&type=packages my scan from https://gist.github.com/cmdcolin/df8e92fe3e82fb2856b5c08d90bf4a32 indicated various shiro subpackages...

I think it requires admin account to do this, so your request there is on a non-admin account and returns status 401. That may be on the right track though!

development effort is geared towards apollo 3 right now, but we certainly would accept PRs to this repo if you have any. if you can post the specific issues that...

if you want to consider hand editing the source code, you can remove or increase this check here which would conditionally display bpPerPx at different scales https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/View/FeatureGlyph/Alignment.js#L72-L78 The 'scale' is...

this doesn't exist yet but it's being worked on with a recent pr here https://github.com/GMOD/jbrowse-components/pull/3648 that pr doesn't have the URL parameter but that should be relatively easy to add...

this is now added to jb2 with the url parameter like &highlight=chr1:1-100 :)

errors like this in your setup log Size.c: loadable library and perl binaries are mismatched (got first handshake key 0xc700080, needed 0xfc00080) have shown up before https://github.com/GMOD/jbrowse/issues/1624 I dunno the...

It would definitely be great to add pangenome "presence absence" (PAV) visualizations one option would be converting your data format from TSV to VCF so that https://github.com/elsiklab/multivariantviewer could interpret that...