Run gemma-wrapper with metadata

1 files changed, 5 insertions, 6 deletions

diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index 8588061..2036adc 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -1,10 +1,10 @@
 #! Run from base dir with
 
-.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
+. .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
 and with some extra paths
 
-.guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- guile -L . -s ./scripts/precompute/precompute-hits.scm
+. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/precompute-hits.scm
 
 You may want to forward a mysql port if there is no DB locally
 
@@ -25,7 +25,6 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org
              )
 
 
-
 ;; potentially you want to test connection with mysql client:
 ;;
 ;;    mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
@@ -59,8 +58,8 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org
      ;; ---- get first available dataset for precompute:
      ;; @@ order by dataid - recurse
 
-     (define (get-trait-name db probeset-id)
-       (dbi-query db (string-append "select Name,Symbol from ProbeSet where Id=" (int-to-string probeset-id) " limit 1"))
+     (define (get-trait db probeset-id)
+       (dbi-query db (string-append "select Id,Chr,Mb,Name,Symbol,description from ProbeSet where Id=" (int-to-string probeset-id) " limit 1"))
        (get-row db)
    )
 
@@ -70,7 +69,7 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org
               (data-id-str (int-to-string data-id))
               (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId"))
               (probeset-id (assoc-ref hit "ProbeSetId"))
-              (trait (get-trait-name db probeset-id))
+              (trait (get-trait db probeset-id))
               (trait-name (assoc-ref trait "Name"))
               (name (dataset-name db probesetfreeze-id))
               ]