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-rw-r--r--gn/runner/gemma.scm11
1 files changed, 7 insertions, 4 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 067800e..d6b08f2 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -12,7 +12,7 @@
run-gemma
))
-(define (run-gemma data-id name trait-name traits)
+(define (run-gemma population data-id name trait-name traits)
(define bxd-inds (geno-inds-bxd "BXD.json"))
(assert (= 235 (length bxd-inds)))
(if name
@@ -40,6 +40,9 @@
;; ---- to start GEMMA precompute inside container
;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
;; --- First we compute K - control output goes to K.json
- (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --name " name " --trait " trait-name " --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt > K.json" ))
- (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --name " name " --trait " trait-name " --verbose --loco --json --debug --parallel --input K.json -- -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json"))
- )
+ (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt > K.json" )))]
+ (if (not (= err 0))
+ (exit err)))
+ (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel --input K.json -- -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json")))]
+ (if (not (= err 0))
+ (exit err))))