From aaff8b8ac968bce9821d6fef22b1296247a9df09 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 24 Feb 2022 13:46:34 +0530
Subject: gn3: Explicitly specify UTF-8 to be the file encoding.

When the encoding is not specified explicitly, the system default encoding is
used. This is not recommended.

* gn3/computations/ctl.py (call_ctl_script),
gn3/computations/gemma.py (generate_pheno_txt_file),
gn3/computations/parsers.py (parse_genofile),
gn3/computations/partial_correlations.py (partial_correlations_fast),
gn3/computations/rqtl.py (process_rqtl_output, process_perm_output),
gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script),
gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file
encoding.
*
tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file),
tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test
for call to open with encoding='utf-8' argument.
---
 guix-system.scm | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

(limited to 'guix-system.scm')

diff --git a/guix-system.scm b/guix-system.scm
index c154d01..7142cea 100644
--- a/guix-system.scm
+++ b/guix-system.scm
@@ -111,10 +111,11 @@ function."
                       %base-file-systems))
   (users %base-user-accounts)
   (packages %base-packages)
-  (services (cons* (service virtuoso-service-type
-                            (virtuoso-configuration
-                             (http-server-port 8891)))
-                   (service genenetwork3-service-type
-                            (genenetwork3-configuration
-                             (port 5000)))
-                   %base-services)))
+  (services (cons*
+             ;; (service virtuoso-service-type
+             ;;          (virtuoso-configuration
+             ;;           (http-server-port 8891)))
+             (service genenetwork3-service-type
+                      (genenetwork3-configuration
+                       (port 5000)))
+             %base-services)))
-- 
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