aboutsummaryrefslogtreecommitdiff
path: root/gn/runner
diff options
context:
space:
mode:
Diffstat (limited to 'gn/runner')
-rw-r--r--gn/runner/gemma.scm5
1 files changed, 3 insertions, 2 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index ff70f57..067800e 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -39,6 +39,7 @@
;; ---- 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
- (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" ))
+ ;; --- 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"))
)