From bc0bc49230c7bfbf2343301345da79a04bff43c9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 24 Sep 2023 15:24:17 +0300
Subject: pggb: Provide version with glibc-hwcaps.

---
 gn/packages/bioinformatics.scm | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c2a2e09..1fb8844 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -20,6 +20,7 @@
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
   #:use-module (gn packages crates-io)
+  #:use-module (gn packages datastructures)
   #:use-module (gn packages java)
   #:use-module (gn packages ocaml)
   #:use-module (gn packages python)
@@ -2602,7 +2603,7 @@ multiple sequence alignment.")
              fastix
              multiqc
              mummer
-             odgi-hwcaps
+             odgi
              pafplot
              parallel
              pigz
@@ -2616,7 +2617,7 @@ multiple sequence alignment.")
              vcfbub
              vcflib
              vg
-             wfmash-hwcaps))
+             wfmash))
       (home-page "https://doi.org/10.1101/2023.04.05.535718")
       (synopsis "PanGenome Graph Builder")
       (description "@command{pggb} builds
@@ -2646,6 +2647,19 @@ Reference Consortium, HPRC} as a method to build a graph from the
 @url{https://doi.org/10.1101/2022.07.09.499321, draft human pangenome}.")
       (license license:expat))))
 
+(define use-glibc-hwcaps
+  (package-input-rewriting/spec
+    ;; Replace some packages with ones built targeting custom packages build
+    ;; with glibc-hwcaps support.
+    `(("sdsl-lite" . ,(const sdsl-lite-hwcaps))
+      ("odgi" . ,(const odgi-hwcaps))
+      ("wfmash" . ,(const wfmash-hwcaps)))))
+
+(define-public pggb-with-hwcaps
+  (package
+    (inherit (use-glibc-hwcaps pggb))
+    (name "pggb-with-hwcaps")))
+
 (define-public ucsc-genome-browser
   (package
     (name "ucsc-genome-browser")
-- 
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