diff options
Diffstat (limited to 'gn/runner/gemma.scm')
| -rw-r--r-- | gn/runner/gemma.scm | 39 |
1 files changed, 23 insertions, 16 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index bcb4c36..2edb7b2 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -21,32 +21,39 @@ (display traits) (newline) ;; ---- write phenotype file - (let* [(port (mkstemp "pheno.txt-XXXXXX")) - (pheno-fn (port-filename port))] - (for-each (lambda (ind) - (begin - (let* [(value (assoc-ref traits ind)) - (outvalue (if value - value - "NA"))] - (display outvalue) - (newline) - (display outvalue port) - (newline port)))) - bxd-inds) - (close port) + (let* [(sys-tmpdir (getenv "TMPDIR")) + (tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX"))) + (pheno-fn (string-append tmpdir "/pheno.txt")) + (k-json-fn (string-append tmpdir "/K.json")) + (gwa-json-fn (string-append tmpdir "/GWA.json"))] + (call-with-output-file pheno-fn + (lambda (port) + (for-each (lambda (ind) + (begin + (let* [(value (assoc-ref traits ind)) + (outvalue (if value + value + "NA"))] + (display outvalue) + (newline) + (display outvalue port) + (newline port)))) + bxd-inds))) ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm ;; ---- 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" )))] + (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 )))] (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-fn " -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 --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) + (delete-file gwa-json-fn) + (delete-file k-json-fn) + (rmdir tmpdir) ) ) |