[Gmod-ajax] Long ago promised features

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[Gmod-ajax] Long ago promised features

Keiran Raine
Resend, hopefully un-garbled

Hi all,

It’s nice to see the GSOC projects getting underway again but I’m wondering when features that were promised in JBrowse 2.0 will ever appear (or JBrowse 2.0) e.g.

  • Native authentication plugins
    • Currently need to generate cookies in another page prior to accessing JBrowse
      • No documentation of what needs to be set
      • Doesn’t handle per-dataset access rights (the drop down most use for species)
    • Provide server details for your site LDAP or single-sign-on services.
    • Specify users or groups that have access in config for datasets.

Also there is heavy support for CRAM (on the GitHub issue #546).  The benefits of CRAM are possibly more far-reaching than many realise, so here’s a list of pros and cons:

Increased load on browser for on-click popups as a record only includes differences from reference seq (if maintaining same display as BAM)

Faster initial load time - indices are compressed by default
Faster general load time - far less data to stream
Better for remote working - more likely to be limited by IO than CPU

I realise that the direction of development is now mostly driven by Apollo but from what I gather most of this work has been prototyped so it would be really great to see it being made available (even if the authentication could just be ported to the current work-stream).

Unfortunately these are fast becoming limiting factors in our continuing use of JBrowse as wrangling development time (in a group with limited JS skills) for something available in a different Genome Browser is challenging.

Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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