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| author | Pjotr Prins | 2024-07-11 12:14:06 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2024-07-11 12:14:06 +0200 |
| commit | b03f0ada0c3e64c16eeba4278d0b8a4470a26b10 (patch) | |
| tree | 2285d7f1d3215ea57c208f1dc9868cda569b71ea /gn/runner/gemma.scm | |
| parent | 84a85da3d4934d43c3caf5cefb660e0d5aaec6f4 (diff) | |
| download | gn-guile-b03f0ada0c3e64c16eeba4278d0b8a4470a26b10.tar.gz | |
Handle genotype filename to pass into gemma-wrapper
Diffstat (limited to 'gn/runner/gemma.scm')
| -rw-r--r-- | gn/runner/gemma.scm | 6 |
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) |