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| author | Pjotr Prins | 2024-01-01 17:47:34 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2024-01-01 17:47:34 +0100 |
| commit | 691eed969ac4bb9fa43358b9a8e0d1ea43accbea (patch) | |
| tree | 69a38708a10b8f525b465332796e636aac9d52e6 /gn/runner/gemma.scm | |
| parent | 0799806735942cc3d44626c3c8b54402343a47f5 (diff) | |
| download | gn-guile-691eed969ac4bb9fa43358b9a8e0d1ea43accbea.tar.gz | |
Run gemma-wrapper with metadata
Diffstat (limited to 'gn/runner/gemma.scm')
| -rw-r--r-- | gn/runner/gemma.scm | 5 |
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")) ) |