diff options
| author | Pjotr Prins | 2023-11-24 09:07:55 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2023-11-24 09:07:55 +0100 |
| commit | fb22ae84c143a27ddc4699327e8aff6c93a0bf6c (patch) | |
| tree | 419c28241bc102e39907a3d9c5897eb428cb418e /gn/runner/gemma.scm | |
| parent | e4cb959730ed5d89c8f5e96de2ddbd405fcf2cc9 (diff) | |
| download | gn-guile-fb22ae84c143a27ddc4699327e8aff6c93a0bf6c.tar.gz | |
Fetch genotype inds from json file
Diffstat (limited to 'gn/runner/gemma.scm')
| -rw-r--r-- | gn/runner/gemma.scm | 9 |
1 files changed, 6 insertions, 3 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 31a14f7..d9e43eb 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -17,13 +17,16 @@ (display traits) (newline) ;; ---- write phenotype file - (call-with-output-file "test.tmp" + (call-with-output-file "pheno.txt" (lambda (port) (write 12 port) (newline port) (write "HELLO" port) )) + ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm - ;; ---- start GEMMA precompute - (system "gemma") + ;; ---- to start GEMMA precompute inside container + ;; env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm + ;; --- First we compute K + (system (string-append "env GEMMA_COMMAND=/gemma/bin/gemma /gemma-wrapper/bin/gemma-wrapper --debug -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" )) ) |