From 70cf276c980ce66f14076196cdba5db6f482bea1 Mon Sep 17 00:00:00 2001
From: pjotr
Date: Sun, 31 May 2026 09:25:31 +0000
Subject: Propagate tools in gemma-wrapper

---
 gn/packages/gemma.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index ce486e6..9b44759 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -19,6 +19,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages parallel)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages textutils)
   #:use-module (gnu packages time)
   #:use-module (gnu packages web)
   #:use-module (gnu packages ruby-check)
@@ -140,8 +141,14 @@ genome-wide association studies (GWAS).")
       (native-inputs (list ruby-rake))
       (inputs (list gemma-gn2))
       (propagated-inputs
-       (list parallel    ;; bin/gemma-wrapper shells out to GNU parallel
-             coreutils)) ;; uses cat
+       ;; bin/gemma-wrapper shells out to all of these; propagate
+       ;; them so `guix shell gemma-wrapper` is a complete runtime.
+       (list parallel      ;; orchestrates per-chromosome and permutation jobs
+             coreutils      ;; uses cat, env, rm
+             tar            ;; archives GEMMA's per-run outputs as .tar.xz
+             xz             ;; tar -J needs xz on PATH
+             time           ;; bin/gemma-wrapper invokes `time -v gemma ...`
+             pfff))         ;; fast file fingerprint for inputs >100KB
       (arguments
        (list
         #:phases
-- 
cgit 1.4.1