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| -rw-r--r-- | README.md | 12 |
1 files changed, 8 insertions, 4 deletions
@@ -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 |