From 84a85da3d4934d43c3caf5cefb660e0d5aaec6f4 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 11 Jul 2024 09:41:10 +0200
Subject: precompute: runner completes

---
 gn/runner/gemma.scm | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

(limited to 'gn/runner/gemma.scm')

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 69991dd..9207316 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -39,24 +39,27 @@
       ))
 )
 
-(define (invoke-gemma-wrapper-loco name trait-name pheno-fn)
+(define (invoke-gemma-wrapper-loco name trait-name trait-fn 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"))]
+         (gwa-json-fn (string-append tmpdir "/GWA.json"))
+         (trait-json-fn (string-append tmpdir "/" trait-fn))]
+    (copy-file trait-fn trait-json-fn)
     ;; --- First we compute K - control output goes to K.json
     (let [(err (system (string-append "/gemma-wrapper/bin/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/bin/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)))]
+    (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --meta \"" trait-json-fn "\" --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --lmdb --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)
+    (delete-file pheno-fn)
+    (delete-file gwa-json-fn)
+    (delete-file k-json-fn)
+    (delete-file trait-json-fn)
+    (rmdir tmpdir)
     )
   )
 
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