diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/data/dataset.scm | 11 | ||||
| -rw-r--r-- | gn/data/genotype.scm | 2 | ||||
| -rw-r--r-- | gn/runner/gemma.scm | 5 |
3 files changed, 10 insertions, 8 deletions
diff --git a/gn/data/dataset.scm b/gn/data/dataset.scm index 3d96663..c28cf25 100644 --- a/gn/data/dataset.scm +++ b/gn/data/dataset.scm @@ -1,11 +1,9 @@ (define-module (gn data dataset) - ;; #:use-module (json) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 iconv) #:use-module (ice-9 receive) #:use-module (ice-9 string-fun) - ;; #:use-module (gn db sparql) #:use-module (dbi dbi) #:use-module (gn db mysql) #:use-module (gn data group) @@ -16,8 +14,11 @@ dataset-name )) -(define (dataset-name db probesetfreeze-id) +(define (get-dataset db probesetfreeze-id) (dbi-query db (string-append - "select Name2 from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;")) - (assoc-ref (get-row db) "Name2")) + "select Name,Name2,FullName from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;")) + (get-row db)) + +(define (dataset-name db probesetfreeze-id) + (assoc-ref (get-dataset db probesetfreeze-id) "Name")) diff --git a/gn/data/genotype.scm b/gn/data/genotype.scm index a12deee..c7cb63c 100644 --- a/gn/data/genotype.scm +++ b/gn/data/genotype.scm @@ -1,5 +1,5 @@ (define-module (gn data genotype) - ;; #:use-module (json) + #:use-module (json) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 iconv) diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index ff70f57..067800e 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -39,6 +39,7 @@ ;; ---- 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 - (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" )) + ;; --- 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")) ) |