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| author | Pjotr Prins | 2024-06-27 05:34:00 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2024-06-27 05:34:00 -0500 |
| commit | 1b37b7738a4c756503ceaaa2645592521abd86f3 (patch) | |
| tree | 6225963cfc2f582b005f78b390b141903028ee99 | |
| parent | 9708991177a8450f8c17dad732f35a4b9c95c287 (diff) | |
| download | gn-guile-1b37b7738a4c756503ceaaa2645592521abd86f3.tar.gz | |
Run gemma-wrapper in a container
| -rw-r--r-- | gn/runner/gemma.scm | 4 | ||||
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 2 |
2 files changed, 3 insertions, 3 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index ec2a4d6..69991dd 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -47,10 +47,10 @@ (k-json-fn (string-append tmpdir "/K.json")) (gwa-json-fn (string-append tmpdir "/GWA.json"))] ;; --- First we compute K - control output goes to K.json - (let [(err (system (string-append "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 BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))] (if (not (= err 0)) (exit err))) - (let [(err (system (string-append "gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --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 --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --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)))] (if (not (= err 0)) (exit err))) ;; (delete-file pheno-fn) diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index 48222b4..e6a4e26 100755 --- a/scripts/precompute/run-gemma.scm +++ b/scripts/precompute/run-gemma.scm @@ -9,7 +9,7 @@ Run from base dir with and with some extra paths (for gemma) -guix shell -C -F xz tar time parallel gemma coreutils-minimal guile guile-dbi guile-json ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -e main -s ./scripts/precompute/run-gemma.scm test +~/opt/guix-pull/bin/guix shell -C -F xz tar time parallel coreutils-minimal guile guile-dbi guile-json ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp GEMMA_COMMAND=/gemma/bin/gemma-0.98.5-linux-static-debug guile -L . -e main -s ./scripts/precompute/run-gemma.scm !# |