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(define-module (gn runner gemma)
#:use-module (json)
#:use-module (ice-9 match)
#:use-module (ice-9 format)
#:use-module (ice-9 iconv)
#:use-module (ice-9 receive)
#:use-module (ice-9 string-fun)
#:export (
run-gemma
))
(define (run-gemma data-id name trait-name traits)
(if name
(display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n")))
(display data-id)
(display traits)
(newline)
;; ---- write phenotype file
(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
;; ---- 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" ))
)
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