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-rw-r--r--gn/packages/bioinformatics.scm4
-rw-r--r--gn/packages/maths.scm108
2 files changed, 111 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 9886e3f..95dda00 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -22,6 +22,7 @@
#:use-module (gn packages crates-io)
#:use-module (gn packages datastructures)
#:use-module (gn packages java)
+ #:use-module (gn packages maths)
#:use-module (gn packages ocaml)
#:use-module (gn packages python)
#:use-module (gnu packages algebra)
@@ -2799,7 +2800,8 @@ Reference Consortium, HPRC} as a method to build a graph from the
(package-input-rewriting/spec
;; Replace some packages with ones built targeting custom packages build
;; with glibc-hwcaps support.
- `(("sdsl-lite" . ,(const sdsl-lite-hwcaps))
+ `(;("gsl" . ,(const gsl-hwcaps)) ; Causes too many rebuilds through multiqc
+ ("sdsl-lite" . ,(const sdsl-lite-hwcaps))
("seqwish" . ,(const seqwish-hwcaps))
("odgi" . ,(const odgi-hwcaps))
("wfmash" . ,(const wfmash-hwcaps)))))
diff --git a/gn/packages/maths.scm b/gn/packages/maths.scm
index 1c1c1ae..7dfb896 100644
--- a/gn/packages/maths.scm
+++ b/gn/packages/maths.scm
@@ -3,6 +3,7 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
+ #:use-module (guix gexp)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gperf)
#:use-module (gnu packages maths)
@@ -131,3 +132,110 @@
(inputs
`(,@(fold alist-delete (package-inputs suitesparse)
'("metis"))))))
+
+(define-public gsl-x86-64-v2
+ (package/inherit gsl
+ (name "gsl-x86-64-v2")
+ (arguments
+ (substitute-keyword-arguments (package-arguments gsl)
+ ((#:make-flags flags #~'())
+ #~(append (list "CFLAGS=-march=x86-64-v2"
+ "CXXFLAGS=-march=x86-64-v2")
+ #$flags))
+ ((#:configure-flags flags #~'())
+ #~(append (list (string-append "--libdir=" #$output
+ "/lib/glibc-hwcaps/x86-64-v2"))
+ #$flags))
+ ;; The building machine can't necessarily run the code produced.
+ ((#:tests? _ #t) #f)
+ ((#:phases phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (add-after 'install 'remove-extra-files
+ (lambda _
+ (delete-file-recursively (string-append #$output "/bin"))
+ (delete-file-recursively (string-append #$output "/include"))))))))
+ (supported-systems '("x86_64-linux"))
+ (properties `((hidden? . #t)
+ (tunable? . #f)))))
+
+(define-public gsl-x86-64-v3
+ (package/inherit gsl
+ (name "gsl-x86-64-v3")
+ (arguments
+ (substitute-keyword-arguments (package-arguments gsl)
+ ((#:make-flags flags #~'())
+ #~(append (list "CFLAGS=-march=x86-64-v3"
+ "CXXFLAGS=-march=x86-64-v3")
+ #$flags))
+ ((#:configure-flags flags #~'())
+ #~(append (list (string-append "--libdir=" #$output
+ "/lib/glibc-hwcaps/x86-64-v3"))
+ #$flags))
+ ;; The building machine can't necessarily run the code produced.
+ ((#:tests? _ #t) #f)
+ ((#:phases phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (add-after 'install 'remove-extra-files
+ (lambda _
+ (delete-file-recursively (string-append #$output "/bin"))
+ (delete-file-recursively (string-append #$output "/include"))))))))
+ (supported-systems '("x86_64-linux"))
+ (properties `((hidden? . #t)
+ (tunable? . #f)))))
+
+(define-public gsl-x86-64-v4
+ (package/inherit gsl
+ (name "gsl-x86-64-v4")
+ (outputs '("out" "static"))
+ (arguments
+ (substitute-keyword-arguments (package-arguments gsl)
+ ((#:make-flags flags #~'())
+ #~(append (list "CFLAGS=-march=x86-64-v4"
+ "CXXFLAGS=-march=x86-64-v4")
+ #$flags))
+ ((#:configure-flags flags #~'())
+ #~(append (list (string-append "--libdir=" #$output
+ "/lib/glibc-hwcaps/x86-64-v4"))
+ #$flags))
+ ;; The building machine can't necessarily run the code produced.
+ ((#:tests? _ #t) #f)
+ ((#:phases phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (add-after 'install 'remove-extra-files
+ (lambda _
+ (delete-file-recursively (string-append #$output "/bin"))
+ (delete-file-recursively (string-append #$output "/include"))))))))
+ (supported-systems '("x86_64-linux"))
+ (properties `((hidden? . #t)
+ (tunable? . #f)))))
+
+;; This copy of gsl will automatically use the libraries that target the
+;; x86_64 psABI which the hardware supports.
+(define-public gsl-hwcaps
+ (package/inherit gsl
+ (name "gsl-hwcaps")
+ (arguments
+ (substitute-keyword-arguments (package-arguments gsl)
+ ((#:phases phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (add-after 'install 'install-optimized-libraries
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((hwcaps "/lib/glibc-hwcaps"))
+ (copy-recursively
+ (string-append (assoc-ref inputs "gsl-x86-64-v2")
+ hwcaps "/x86-64-v2")
+ (string-append #$output hwcaps "/x86-64-v2"))
+ (copy-recursively
+ (string-append (assoc-ref inputs "gsl-x86-64-v3")
+ hwcaps "/x86-64-v3")
+ (string-append #$output hwcaps "/x86-64-v3"))
+ (copy-recursively
+ (string-append (assoc-ref inputs "gsl-x86-64-v4")
+ hwcaps "/x86-64-v4")
+ (string-append #$output hwcaps "/x86-64-v4")))))))))
+ (native-inputs
+ (modify-inputs (package-native-inputs gsl)
+ (append gsl-x86-64-v2
+ gsl-x86-64-v3
+ gsl-x86-64-v4)))
+ (properties `((tunable? . #f)))))