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| author | zsloan | 2022-12-23 14:12:39 -0600 |
|---|---|---|
| committer | GitHub | 2022-12-23 14:12:39 -0600 |
| commit | 4081d30cf8a41f876f8fab0c7a03d359bc438f94 (patch) | |
| tree | 27e3cd1087de5369b1c54491b06649c788275874 | |
| parent | 5b9d65907a3904cfce42294edf319d85f43333e5 (diff) | |
| download | genenetwork3-4081d30cf8a41f876f8fab0c7a03d359bc438f94.tar.gz | |
Update how to set configurations in README
| -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 |