Tracking metadat for GN DB

2 files changed, 9 insertions, 5 deletions

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index d86abd7..89b6482 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -1,6 +1,7 @@
 (define-module (gn runner gemma)
   #:use-module (json)
   #:use-module (gn data genotype)
+  #:use-module (gn util convert)
   #:use-module (ice-9 match)
   #:use-module (ice-9 format)
   #:use-module (ice-9 iconv)
@@ -12,13 +13,16 @@
             run-gemma
             ))
 
-(define (run-gemma population data-id name trait-name traits)
+(define (run-gemma population data-id probeset-id probesetfreeze-id name trait-name traits)
   "Run gemma-wrapper to compute GRM and GWA. On failure the run will stop(!)"
   (define bxd-inds (geno-inds-bxd "BXD.json"))
+  (define ids (string-append (int-to-string data-id) ","
+                             (int-to-string probeset-id) ","
+                             (int-to-string probesetfreeze-id)))
   (assert (= 235 (length bxd-inds)))
   (if name
       (display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n")))
-  (display data-id)
+  (display ids)
   (display traits)
   (newline)
   ;; ---- write phenotype file
@@ -51,7 +55,7 @@
     (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 --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 "\" --id \"" ids "\" --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)
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index f33e7e9..8f27bbe 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -99,12 +99,12 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org
                                    ((id . value) (cons (assoc-ref bxd-strains id) value)
                                     )))
                                id_traits))
-               (display traits)
+               ;; (display traits)
                ;; (if (= 0 (length non-bxd))
                (if (eq? non-bxd '())
                    (begin
                      (set-precompute-hit-status! db data-id-str "GEMMA-START")
-                     (run-gemma "BXD" data-id name trait-name traits)
+                     (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits)
                      (set-precompute-hit-status! db data-id-str "GEMMA-DONE"))
                    ;; disable precompute if non-bxd, for now, so it won't try again
                    (set-precompute-hit-status! db data-id-str "NON-BXD"))