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| author | Pjotr Prins | 2024-01-05 12:09:51 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2024-01-05 12:09:51 +0100 |
| commit | 902cf907e9b315f52b2ef3b4b791e492a87e6437 (patch) | |
| tree | 6e3b86f502c8521e1cedf98b963e86723aafe150 | |
| parent | c222420ac526115324e259b5e89bb1c56d39b4cd (diff) | |
| download | gn-guile-902cf907e9b315f52b2ef3b4b791e492a87e6437.tar.gz | |
Remove extra check and debug flag for gemma run
| -rw-r--r-- | gn/data/hits.scm | 2 | ||||
| -rw-r--r-- | gn/runner/gemma.scm | 4 |
2 files changed, 3 insertions, 3 deletions
diff --git a/gn/data/hits.scm b/gn/data/hits.scm index 29d377b..94b4749 100644 --- a/gn/data/hits.scm +++ b/gn/data/hits.scm @@ -27,7 +27,7 @@ On completion it is set to 'GEMMA-DONE'. This is a temporary measure to get precompute going. Note we are counting on automated MariaDB transactions to not compete." - (dbi-query db (string-append "UPDATE ProbeSetXRef SET Locus_old=\"" status-str "\" WHERE DataId=" data-id-str " AND Locus_old is NULL")) + (dbi-query db (string-append "UPDATE ProbeSetXRef SET Locus_old=\"" status-str "\" WHERE DataId=" data-id-str)) (ensure db) ) diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index a31846a..d86abd7 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -48,10 +48,10 @@ ;; ---- 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 - (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-fn " -a BXD.8_snps.txt > " k-json-fn )))] + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --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 "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -maf 0.1 > " gwa-json-fn)))] + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -maf 0.1 > " gwa-json-fn)))] (if (not (= err 0)) (exit err))) (delete-file pheno-fn) |