From 691eed969ac4bb9fa43358b9a8e0d1ea43accbea Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 1 Jan 2024 17:47:34 +0100
Subject: Run gemma-wrapper with metadata

---
 gn/runner/gemma.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gn/runner/gemma.scm')

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"))
   )
-- 
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