From 4081d30cf8a41f876f8fab0c7a03d359bc438f94 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 23 Dec 2022 14:12:39 -0600
Subject: Update how to set configurations in README

---
 README.md | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index fefc9c6..537e170 100644
--- a/README.md
+++ b/README.md
@@ -95,11 +95,15 @@ and try again. Also make sure your ~/guix-bioinformatics is up to date.
 
 See also instructions in [.guix.scm](.guix.scm).
 
-#### Setting necessary environment variables
+#### Setting necessary configurations
 
-At least the following two need to be set for R/qtl to work (there might be others which I'll add if they come up):
-RQTL_WRAPPER (should be in genenetwork3/scripts/rqtl_wrapper.R)
-TMPDIR (where the rqtl_wrapper.R cross files are generated, used by the R script)
+These configurations should be set in an external config file, pointed to with the environment variable GN3_CONF.
+
+- SPARQL_ENDPOINT (ex: "http://localhost:9082/sparql")
+- RQTL_WRAPPER (ex: "~/genenetwork3/scripts/rqtl_wrapper.R")
+- XAPIAN_DB_PATH (ex: "/export/data/genenetwork/xapian")
+
+TMPDIR also needs to be set correctly for the R script(s) (previously there was an issue with it being set to /tmp instead of ~/genenetwork3/tmp)
 
 ## Migrations
 
-- 
cgit v1.2.3