Sim1000G installation patch

[williambrandler]

Signed-off-by: William Brandler william.brandler@databricks.com

What changes are proposed in this pull request?

The current solution for simulating genotypes using Spark is fairly rudimentary. Fixing the installation of Sim1000G as a replacement so we can ramp up testing. Having the tool working with the Glow Docker Container makes it much easier to iterate

I was getting this issue:

`Loading required package: hapsim Loading required package: MASS Loading required package: stringr Loading required package: readr [#.......] Reading VCF file.. Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1

Error : Unknown TZ /UTC Some( Error: Unknown TZ /UTC )`

Gonna patch this into projectglow/databricks-glow:1.1.2

Note: in the end this didn't work, you have to manually add

options(tz="UTC")
Sys.setenv(TZ="UTC")

before loading the library, replacing UTC with your timezone.

How is this patch tested?

• [ ] Manual tests

(Details)

[codecov[bot]]

Codecov Report

Merging #482 (b7d123a) into master (6c28c02) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #482   +/-   ##
=======================================
  Coverage   93.66%   93.66%           
=======================================
  Files          95       95           
  Lines        4875     4875           
  Branches      457      457           
=======================================
  Hits         4566     4566           
  Misses        309      309           

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 6c28c02...b7d123a. Read the comment docs.