Precompute will run gemma and update the DB status

1 files changed, 6 insertions, 2 deletions

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 2edb7b2..a31846a 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -13,10 +13,11 @@
             ))
 
 (define (run-gemma population data-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"))
   (assert (= 235 (length bxd-inds)))
   (if name
-      (display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n")))
+      (display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n")))
   (display data-id)
   (display traits)
   (newline)
@@ -38,7 +39,9 @@
                         (newline)
                         (display outvalue port)
                         (newline port))))
-                  bxd-inds)))
+                  bxd-inds)
+        (close port)
+       ))
 
     ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
@@ -56,4 +59,5 @@
     (delete-file k-json-fn)
     (rmdir tmpdir)
     )
+  #t
   )