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| author | Munyoki Kilyungi | 2025-09-16 11:31:17 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2025-09-19 15:36:05 +0300 |
| commit | 8450a308c1edf84243d957098effd85c749d2ae1 (patch) | |
| tree | d97f374744faebc152af47fbdf6013b56a9327a1 | |
| parent | 621e7133c7de98e45d2a6a6c060559b2837e25e4 (diff) | |
| download | gn-machines-8450a308c1edf84243d957098effd85c749d2ae1.tar.gz | |
Set environment variables for GN2.
| -rw-r--r-- | genenetwork-development.scm | 13 |
1 files changed, 13 insertions, 0 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index a11bc56..8441c93 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -514,6 +514,7 @@ server described by CONFIG, a <genenetwork-configuration> object." (invoke "git" "log" "--max-count" "1") (hline)) + (setenv "TERM" "xterm-256color") ;; Clone the latest genenetwork2 ;; repositories. (with-directory-excursion @@ -536,6 +537,18 @@ server described by CONFIG, a <genenetwork-configuration> object." (setenv "REQUESTS_CA_BUNDLE" (string-append (getenv "GN2_PROFILE") "/etc/ssl/certs/ca-certificates.crt")) + (setenv "PYTHONPATH" (string-append + (getenv "GN2_PROFILE") + "/lib/python3.11/site-packages")) + (setenv "PATH" (string-append (getenv "GN2_PROFILE") "/bin:$PATH")) + (setenv "R_LIBS_SITE" (string-append (getenv "GN2_PROFILE") "/site-library")) + (setenv "JS_GUIX_PATH" (string-append (getenv "GN2_PROFILE") "/share/genenetwork2/javascript")) + (setenv "GUIX_GENENETWORK_FILES" (string-append (getenv "GN2_PROFILE") "/share/genenetwork2")) + (setenv "GENENETWORK_FILES" #$genotype-files) + (setenv "PLINK_COMMAND" (string-append (getenv "GN2_PROFILE") "/bin/plink2")) + (setenv "GEMMA_COMMAND" (string-append (getenv "GN2_PROFILE") "/bin/gemma")) + (setenv "GEMMA_WRAPPER_COMMAND" (string-append (getenv "GN2_PROFILE") "/bin/gemma-wrapper")) + (setenv "HOME" "/tmp") (setenv "GN2_SETTINGS" #$(mixed-text-file "gn2.conf" |