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authorEfraim Flashner2023-09-24 15:24:17 +0300
committerEfraim Flashner2023-09-24 15:24:17 +0300
commitbc0bc49230c7bfbf2343301345da79a04bff43c9 (patch)
treecb4f0c0672f9efaaee7806c3d4e4a09c3b78310c /gn/packages/bioinformatics.scm
parent10f65dc422f98e2d679754e194ea7c70328b7784 (diff)
downloadguix-bioinformatics-bc0bc49230c7bfbf2343301345da79a04bff43c9.tar.gz
pggb: Provide version with glibc-hwcaps.
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm18
1 files changed, 16 insertions, 2 deletions
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")