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| -rw-r--r-- | README.md | 6 |
1 files changed, 4 insertions, 2 deletions
diff --git a/README.md b/README.md index 78b7be5..d22948c 100644 --- a/README.md +++ b/README.md @@ -43,8 +43,9 @@ There are at least three ways to start GeneNetwork3 with GNU Guix: 1. Create an environment with `guix shell` 2. Create a container with `guix shell -C` 3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile` +4. Use the guix system container with GN3 directory mounted in -At this point we use all three for different purposes. +At this point we use all three for different purposes. In all cases you'll most likely need the mysql database. #### Create an environment: @@ -123,8 +124,9 @@ These configurations should be set in an external config file, pointed to with t - SPARQL_ENDPOINT (ex: "http://localhost:9082/sparql") - RQTL_WRAPPER (ex: "~/genenetwork3/scripts/rqtl_wrapper.R") - XAPIAN_DB_PATH (ex: "/export/data/genenetwork/xapian") +- TMPDIR -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) +TMPDIR also needs to be set correctly for the R script(s) because they pass results on as files on the local system (previously there was an issue with it being set to /tmp instead of ~/genenetwork3/tmp) ## Command-Line Utility Scripts |