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-rw-r--r--gn/runner/gemma.scm6
1 files changed, 3 insertions, 3 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 9207316..9a5c0fc 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -39,7 +39,7 @@
))
)
-(define (invoke-gemma-wrapper-loco name trait-name trait-fn pheno-fn)
+(define (invoke-gemma-wrapper-loco name trait-name trait-fn pheno-fn geno-fn)
"Create a tmpdir and invoke gemma-wrapper using parallel LOCO. Note that at this point we use a number of defaults for BXD"
(let* [(population "BXD")
(sys-tmpdir (getenv "TMPDIR"))
@@ -49,10 +49,10 @@
(trait-json-fn (string-append tmpdir "/" trait-fn))]
(copy-file trait-fn trait-json-fn)
;; --- First we compute K - control output goes to K.json
- (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))]
+ (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g " geno-fn " -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))]
(if (not (= err 0))
(exit err)))
- (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --meta \"" trait-json-fn "\" --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --lmdb --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
+ (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --meta \"" trait-json-fn "\" --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --lmdb --input " k-json-fn " -- -g " geno-fn " -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
(if (not (= err 0))
(exit err)))
(delete-file pheno-fn)