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authorMuriithi Frederick Muriuki2021-08-30 07:00:38 +0300
committerMuriithi Frederick Muriuki2021-08-30 07:00:38 +0300
commit983acfdfc523677b4d7501287a000b7fd52a2c39 (patch)
tree92547cd368fd0f024d4aedf92b1c3dc62417e65d /gn3/settings.py
parentc045122908d36bba4ca197f3f67e89d80958f38f (diff)
downloadgenenetwork3-983acfdfc523677b4d7501287a000b7fd52a2c39.tar.gz
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.
Diffstat (limited to 'gn3/settings.py')
-rw-r--r--gn3/settings.py3
1 files changed, 3 insertions, 0 deletions
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"))