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| author | Pjotr Prins | 2024-01-04 12:51:45 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2024-01-04 12:51:45 +0100 |
| commit | 0721d15f275ce9abd55e60955265997f0e39db3d (patch) | |
| tree | 31a7e79c2c4697f4d5ecadb8f391b9380c944942 /gn/runner | |
| parent | 691eed969ac4bb9fa43358b9a8e0d1ea43accbea (diff) | |
| download | gn-guile-0721d15f275ce9abd55e60955265997f0e39db3d.tar.gz | |
Call precompute with population name - BXD only, for now
Diffstat (limited to 'gn/runner')
| -rw-r--r-- | gn/runner/gemma.scm | 11 |
1 files changed, 7 insertions, 4 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 067800e..d6b08f2 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -12,7 +12,7 @@ run-gemma )) -(define (run-gemma data-id name trait-name traits) +(define (run-gemma population data-id name trait-name traits) (define bxd-inds (geno-inds-bxd "BXD.json")) (assert (= 235 (length bxd-inds))) (if name @@ -40,6 +40,9 @@ ;; ---- 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 - 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")) - ) + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --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" )))] + (if (not (= err 0)) + (exit err))) + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --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")))] + (if (not (= err 0)) + (exit err)))) |