diff options
| -rw-r--r-- | gn/runner/gemma.scm | 6 | ||||
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 4 |
2 files changed, 5 insertions, 5 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) diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index 9a7bba2..b0db622 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) -~/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 +~/opt/guix-pull/bin/guix shell -C -F xz python python-lmdb 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 test !# @@ -54,5 +54,5 @@ Usage: list-traits-to-compute [options...] (pheno-fn (string-append trait-id "-pheno.txt")) ] (write-pheno-file pheno-fn traits) - (invoke-gemma-wrapper-loco dataset-name trait-name trait-fn pheno-fn) + (invoke-gemma-wrapper-loco dataset-name trait-name trait-fn pheno-fn "BXD.8_geno.txt.gz") )))))) |