Call precompute with population name - BXD only, for now

4 files changed, 39 insertions, 8 deletions

diff --git a/.guix-shell b/.guix-shell
index 6e68054..d5e9c38 100755
--- a/.guix-shell
+++ b/.guix-shell
@@ -4,4 +4,4 @@
 
 echo "Create a shell to run tools."
 
-guix shell  -L ~/guix-bioinformatics -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel tar xz python python-lmdb python-cffi gemma-gn2 $*
+guix shell  -L ~/guix-bioinformatics -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel tar xz python python-lmdb python-cffi time gemma-gn2 $*
diff --git a/gn/data/population.scm b/gn/data/population.scm
new file mode 100644
index 0000000..46ef04c
--- /dev/null
+++ b/gn/data/population.scm
@@ -0,0 +1,28 @@
+(define-module (gn data population)
+  #: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 data group)
+  #:use-module (gn db mysql)
+  #:use-module (gn util convert)
+  #:use-module (web gn-uri)
+
+  #:export (
+            population-info
+            ))
+
+(define* (population-info id)
+  "
+Return population (InbredSet) info by GN ID
+"
+  (call-with-db
+   (lambda (db)
+     (dbi-query db (string-append
+                    "SELECT InbredSetId,InbredSetName,Name,SpeciesId,FullName WHERE"
+                    (int-to-string id) " LIMIT 1"))
+     (get-row db))))
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 067800e..d6b08f2 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -12,7 +12,7 @@
             run-gemma
             ))
 
-(define (run-gemma data-id name trait-name traits)
+(define (run-gemma population data-id name trait-name traits)
   (define bxd-inds (geno-inds-bxd "BXD.json"))
   (assert (= 235 (length bxd-inds)))
   (if name
@@ -40,6 +40,9 @@
   ;; ---- 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
-  (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"))
-  )
+  (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.txt -a BXD.8_snps.txt > K.json"  )))]
+    (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.txt -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json")))]
+    (if (not (= err 0))
+        (exit err))))
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index 2036adc..0fabe8f 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -44,9 +44,9 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org
      ;(let [(result (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))]
      ;  (display (car result)))
 
-     ;(newline)
+     ;; ---- fetch all known BXD sample/individual/strain names
      (define bxd-strains (bxd-strain-id-names #:map? #t))
-                                        ;(display (assoc 64728 bxd-strains))
+     ;(display (assoc 64728 bxd-strains))
      ;(newline)
      ;(newline)
      ;(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3")
@@ -103,7 +103,7 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org
          (if (eq? non-bxd '())
              (begin
                (set-precompute-hit-status! db data-id-str "GEMMA-START")
-               (run-gemma data-id name trait-name traits)))
+               (run-gemma "BXD" data-id name trait-name traits)))
              ;; disable precompute if non-bxd, for now, so it won't try again
              (set-precompute-hit-status! db data-id-str "NON-BXD")
          ;;(run-precompute db data-id)