From 41735d8fbf4fbd0d137224f25b20cda6556ad484 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 18 Jun 2024 05:16:42 -0500
Subject: Started on run-gemma

---
 scripts/precompute/precompute-hits.scm |  8 ++++++-
 scripts/precompute/run-gemma.scm       | 42 ++++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 1 deletion(-)
 create mode 100755 scripts/precompute/run-gemma.scm

(limited to 'scripts')

diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index 8f27bbe..a18b33d 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -1,4 +1,10 @@
-#! Run from base dir with
+#! Precompute hits
+
+This is the obsolete script to compute GEMMA directly from the DB. We have split out
+this step into fetching traits and running gemma without DB. This allows scaling up
+on HPC etc.
+
+Run from base dir with
 
 . .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm
new file mode 100755
index 0000000..b14927a
--- /dev/null
+++ b/scripts/precompute/run-gemma.scm
@@ -0,0 +1,42 @@
+#! Run GEMMA
+
+A simple script that takes the JSON input from list-traits-to-compute and runs
+GEMMA on those.
+
+Run from base dir with
+
+guix shell guile guile-dbi -- guile -L ../.. -s run-gemma.scm --help
+
+and with some extra paths
+
+. .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
+
+!#
+
+(use-modules ; (gn data dataset)
+             ; (gn data hits)
+             ; (gn data strains)
+             ; (gn util convert)
+             (gn runner gemma)
+             (ice-9 getopt-long)
+             (ice-9 match)
+             (ice-9 textual-ports)
+             (json)
+             (rnrs bytevectors)
+             (srfi srfi-1)
+             )
+
+(define (main args)
+  ;; (write args)
+  (let* [
+         (option-spec '( (version (single-char #\v) (value #f))
+                         (help    (single-char #\h) (value #f))))
+         (options (getopt-long args option-spec))
+         (help-wanted (option-ref options 'help #f))]
+    (if help-wanted
+        (format #t "list-traits-to-compute writes JSON traits files from the GN DB
+Usage: list-traits-to-compute [options...]
+  -h, --help          Display this help
+")
+  (display "gemma-run")
+)))
-- 
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