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authorPjotr Prins2023-12-02 16:45:55 -0600
committerPjotr Prins2023-12-02 16:45:55 -0600
commit8fb091769b6b01d476b45943bac54a26a8923573 (patch)
tree94569831fcfccb3680dfe47cff41efb01c53278b /gn
parent186da1d636f88421d1bbca0033e2d99a3b15e6cd (diff)
downloadgn-guile-8fb091769b6b01d476b45943bac54a26a8923573.tar.gz
Run gemma
Diffstat (limited to 'gn')
-rw-r--r--gn/runner/gemma.scm20
1 files changed, 14 insertions, 6 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 67dae54..ff70f57 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -23,14 +23,22 @@
;; ---- write phenotype file
(call-with-output-file "pheno.txt"
(lambda (port)
- (write 12 port)
- (newline port)
- (write "HELLO" port)
- ))
+ (for-each (lambda (ind)
+ (begin
+ (let* [(value (assoc-ref traits ind))
+ (outvalue (if value
+ value
+ "NA"))]
+ (display outvalue)
+ (newline)
+ (display outvalue port)
+ (newline port))))
+ bxd-inds)))
+
;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
;; ---- to start GEMMA precompute inside container
- ;; env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
+ ;; env TMPDIR=. LD_LIBRARY_PATH=$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" ))
+ (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" ))
)