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-rw-r--r--gn/runner/gemma.scm9
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" ))
)