diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 93 |
1 files changed, 93 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 75449f3..a303baf 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -195,6 +195,99 @@ accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.") (license license:gpl3))) +(define-public wfmash-x86-64-v2 + (package/inherit wfmash + (name "wfmash-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public wfmash-x86-64-v3 + (package/inherit wfmash + (name "wfmash-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + #;(properties `((hidden? . #t))))) + +(define-public wfmash-x86-64-v4 + (package/inherit wfmash + (name "wfmash-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +;; This copy of wfmash will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public wfmash-hwcaps + (package/inherit wfmash + (name "wfmash-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs wfmash) + (append wfmash-x86-64-v2 + wfmash-x86-64-v3 + wfmash-x86-64-v4))))) + (define-public freec (package (name "control-freec") |