Simplified gemma runner

2 files changed, 28 insertions, 5 deletions

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 4c1c374..ec2a4d6 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -11,6 +11,7 @@
 
   #:export (
             write-pheno-file
+            invoke-gemma-wrapper-loco
             run-gemma
             ))
 
@@ -27,8 +28,10 @@
                   (outvalue (if value
                                 value
                                 "NA"))]
-             (format #t "~s ~s" ind outvalue)
-             (newline)
+             (if value
+                 (begin
+                   (format #t "~s ~s" ind outvalue)
+                   (newline)))
              (display outvalue port)
              (newline port))))
        bxd-inds)
@@ -36,6 +39,27 @@
       ))
 )
 
+(define (invoke-gemma-wrapper-loco name trait-name pheno-fn)
+  "Create a tmpdir and invoke gemma-wrapper using parallel LOCO. Note that at this point we use a number of defaults for BXD"
+  (let* [(population "BXD")
+         (sys-tmpdir (getenv "TMPDIR"))
+         (tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX")))
+         (k-json-fn (string-append tmpdir "/K.json"))
+         (gwa-json-fn (string-append tmpdir "/GWA.json"))]
+    ;; --- First we compute K - control output goes to K.json
+    (let [(err (system (string-append "gemma-wrapper --verbose --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 "gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
+      (if (not (= err 0))
+          (exit err)))
+    ;; (delete-file pheno-fn)
+    ;; (delete-file gwa-json-fn)
+    ;; (delete-file k-json-fn)
+    ;; (rmdir tmpdir)
+    )
+  )
+
 (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 ids (string-append (int-to-string data-id) ","
@@ -46,7 +70,6 @@
   (display ids)
   (display traits)
   (newline)
-  ;; ---- write phenotype file
   (let* [(sys-tmpdir (getenv "TMPDIR"))
          (tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX")))
          (pheno-fn (string-append tmpdir "/pheno.txt"))
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm
index 36edf8b..48222b4 100755
--- a/scripts/precompute/run-gemma.scm
+++ b/scripts/precompute/run-gemma.scm
@@ -9,7 +9,7 @@ Run from base dir with
 
 and with some extra paths (for gemma)
 
-. .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/run-gemma.scm
+guix shell -C -F xz tar time parallel gemma coreutils-minimal guile guile-dbi guile-json 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 . -e main -s ./scripts/precompute/run-gemma.scm test
 
 !#
 
@@ -49,5 +49,5 @@ Usage: list-traits-to-compute [options...]
                  ]
             (display dataset)
             (write-pheno-file "pheno.txt" traits)
-                                        ; (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits)))
+            (invoke-gemma-wrapper-loco dataset-name trait-name "pheno.txt")
           ))))))