From 6fa4d04cf954bc374a8532d285496760f2283f38 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 4 Jan 2024 16:47:24 +0100
Subject: Use tmpdir and tmp files for transient data

---
 gn/runner/gemma.scm | 39 +++++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 16 deletions(-)

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

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index bcb4c36..2edb7b2 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -21,32 +21,39 @@
   (display traits)
   (newline)
   ;; ---- write phenotype file
-  (let* [(port (mkstemp "pheno.txt-XXXXXX"))
-         (pheno-fn (port-filename port))]
-    (for-each (lambda (ind)
-                (begin
-                  (let* [(value (assoc-ref traits ind))
-                         (outvalue (if value
-                                       value
-                                       "NA"))]
-                    (display outvalue)
-                    (newline)
-                    (display outvalue port)
-                    (newline port))))
-              bxd-inds)
-    (close port)
+  (let* [(sys-tmpdir (getenv "TMPDIR"))
+         (tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX")))
+         (pheno-fn (string-append tmpdir "/pheno.txt"))
+         (k-json-fn (string-append tmpdir "/K.json"))
+         (gwa-json-fn (string-append tmpdir "/GWA.json"))]
+    (call-with-output-file pheno-fn
+      (lambda (port)
+        (for-each (lambda (ind)
+                    (begin
+                      (let* [(value (assoc-ref traits ind))
+                             (outvalue (if value
+                                           value
+                                           "NA"))]
+                        (display outvalue)
+                        (newline)
+                        (display outvalue port)
+                        (newline port))))
+                  bxd-inds)))
 
     ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
     ;; ---- 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
-    (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-fn " -a BXD.8_snps.txt > K.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-fn " -a BXD.8_snps.txt > " k-json-fn  )))]
       (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-fn " -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 --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -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)
     )
   )
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