diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 4 | ||||
| -rw-r--r-- | gn/packages/maths.scm | 108 |
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))))) |