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Install from scratch #1093

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davmlaw opened this issue Jun 19, 2024 · 3 comments
Closed

Install from scratch #1093

davmlaw opened this issue Jun 19, 2024 · 3 comments
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@davmlaw

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@davmlaw
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davmlaw commented Jun 19, 2024 •
edited

Haven't done this for 6-12 months

  • Spin up a brand new VM
  • Make sure installation instructions actually work
  • Fix wiki etc
  • Update database dump on vg.com and in wiki (with date and version etc)

We could also try and simplify stuff here if possible

Once this is done, send message to Patto - so he can try setting up a deployment
@davmlaw
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davmlaw commented Jul 5, 2024

I'm downloading VEP 112 on /data/annotation/VEP on vg test

Can create a new VM and connect to that

@davmlaw davmlaw self-assigned this Jul 5, 2024
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - Bump bgzip versions so it installs in Python3.11 and later
d0bb1db
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - bump matplotlib - comment on version freeze was newer o…
6e8a6f1 
…nes break 3.11 - confirming that latest matplotlib (3.9.1) works fine now on 3.11 and 3.12

Had to fix a deprecated method, tested chrom graphs still work
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - missing from requirements
50c598d
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - postgres15+ requires explicit permission for public schema
625282f
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - postgres15+ requires explicit permission for public sch…
7ae5327 
…ema - this needs to be on the database not global
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - numpy removed NaN for nan
4792e01
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - Add examples of how to customise VEP in settings template
ed386d7
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - Remove historical managment commands about library/tool…
22c0898 
… upgrades as now covered with deployment_check
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1093 - Skip this for new deploys
9122838
@davmlaw
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davmlaw commented Jul 12, 2024 •
edited

  • I've made dump and updated wiki

TODO:

  • variantgrid/scripts/install/ubuntu_20_install_dependencies.sh Should have Python stuff removed from it as we are using virtualenv
  • The wiki virtualenv page has Python 3.11 - maybe take the 3.11 out for 3 and make a general env page
  • Move postgres to /data/databases/postgres etc
  • Alter test.variantgrid.com domain name
  • system services have /mnt and /opt but should probably have something to use env/bin/gunicorn etc rather than system ones

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davmlaw commented Aug 8, 2024

Updated wiki, install scripts and DB dump

@davmlaw davmlaw closed this as completed Aug 8, 2024
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