From 1ed1bcb79144a8c60092f19db9dd4eaeff7d18e6 Mon Sep 17 00:00:00 2001
From: pjotr
Date: Thu, 7 May 2026 11:39:23 +0000
Subject:   Summary:

  Added vg-1.71 to factory/guix-bioinformatics/gn/packages/pangenome.scm immediately after the existing vg
   (v1.72.0). It inherits everything (build phases, native-inputs, inputs, synopsis, description, license,
   properties) and only overrides version and source. The origin must repeat the snippet because
  overriding source replaces the parent's whole origin record.

  - Source: https://github.com/vgteam/vg/releases/download/v1.71.0/vg-v1.71.0.tar.gz
  - sha256: 06ag9gb57wjvmxy4pzvskpkph6i6jvs0vy8rjm1xdk3g76l8vhjb
  - guix package -A '^vg' now lists both vg 1.72.0 and vg 1.71.0.
  - Workshop materials can pin via guix shell vg@1.71.0 or by referencing the vg-1.71 symbol directly from
   a manifest.
---
 gn/packages/pangenome.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index af5d9de..e2a1fa1 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -1412,6 +1412,30 @@ multiple sequence alignment.")
         license:zlib
         license:boost1.0))))
 
+(define-public vg-1.71
+  ;; Older release pinned for the pangenome workshop material; the
+  ;; build customisation is identical to vg above so we inherit it
+  ;; and only override version + source (origin must repeat the
+  ;; snippet because overriding source replaces it whole).
+  (package
+    (inherit vg)
+    (version "1.71.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/vgteam/vg/releases/download/v"
+                            version "/vg-v" version ".tar.gz"))
+        (sha256
+         (base32 "06ag9gb57wjvmxy4pzvskpkph6i6jvs0vy8rjm1xdk3g76l8vhjb"))
+        (snippet
+         #~(begin
+             (use-modules (guix build utils))
+             (substitute* (find-files "." "(CMakeLists\\.txt|Makefile)")
+               (("-march=native") "")
+               (("-mtune=native") "")
+               (("-msse4.2") "")
+               (("-mcx16") ""))))))))
+
 (define-public bandage-ng
   (package
     (name "bandage-ng")
-- 
cgit 1.4.1