From 691eed969ac4bb9fa43358b9a8e0d1ea43accbea Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 1 Jan 2024 17:47:34 +0100
Subject: Run gemma-wrapper with metadata

---
 gn/data/dataset.scm  | 11 ++++++-----
 gn/data/genotype.scm |  2 +-
 gn/runner/gemma.scm  |  5 +++--
 3 files changed, 10 insertions(+), 8 deletions(-)

(limited to 'gn')

diff --git a/gn/data/dataset.scm b/gn/data/dataset.scm
index 3d96663..c28cf25 100644
--- a/gn/data/dataset.scm
+++ b/gn/data/dataset.scm
@@ -1,11 +1,9 @@
 (define-module (gn data dataset)
-  ;; #: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 db mysql)
   #:use-module (gn data group)
@@ -16,8 +14,11 @@
             dataset-name
             ))
 
-(define (dataset-name db probesetfreeze-id)
+(define (get-dataset db probesetfreeze-id)
   (dbi-query db
              (string-append
-              "select Name2 from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;"))
-  (assoc-ref (get-row db) "Name2"))
+              "select Name,Name2,FullName from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;"))
+  (get-row db))
+
+(define (dataset-name db probesetfreeze-id)
+  (assoc-ref (get-dataset db probesetfreeze-id) "Name"))
diff --git a/gn/data/genotype.scm b/gn/data/genotype.scm
index a12deee..c7cb63c 100644
--- a/gn/data/genotype.scm
+++ b/gn/data/genotype.scm
@@ -1,5 +1,5 @@
 (define-module (gn data genotype)
-  ;; #:use-module (json)
+  #:use-module (json)
   #:use-module (ice-9 match)
   #:use-module (ice-9 format)
   #:use-module (ice-9 iconv)
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index ff70f57..067800e 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -39,6 +39,7 @@
 
   ;; ---- 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
-  (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt"  ))
+  ;; --- 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"))
   )
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