From 983acfdfc523677b4d7501287a000b7fd52a2c39 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 30 Aug 2021 07:00:38 +0300
Subject: Implement module for interfacing with rust-qtlreaper

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/computations/heatmap.py: move `generate_traits_file` function to new
  module
* gn3/computations/qtlreaper.py: new module to interface with the
  `rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
  utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
  use functions in new module.

  Provide a module with functions to be used to interface with
  `rust-qtlreaper`. This module essentially contains all the functions that
  are needed to build the files needed for, and to run the qtlreaper utility.
---
 gn3/settings.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gn3/settings.py')

diff --git a/gn3/settings.py b/gn3/settings.py
index f4866d5..d137370 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -24,3 +24,6 @@ GN2_BASE_URL = "http://www.genenetwork.org/"
 
 # biweight script
 BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
+
+# qtlreaper command
+REAPER_COMMAND = "{}/bin/qtlreaper".format(os.environ.get("GUIX_ENVIRONMENT"))
-- 
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