diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 119 |
1 files changed, 119 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 50c207d..15d8811 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1687,6 +1687,124 @@ dictionaries to record a queryable version of the graph.") (properties `((tunable? . #t))) (license license:expat))) +(define-public seqwish-x86-64-v2 + (package/inherit seqwish + (name "seqwish-x86-64-v2") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#: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 #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public seqwish-x86-64-v3 + (package/inherit seqwish + (name "seqwish-x86-64-v3") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$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-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public seqwish-x86-64-v4 + (package/inherit seqwish + (name "seqwish-x86-64-v4") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#: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 #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +;; This copy of seqwish will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public seqwish-hwcaps + (package/inherit seqwish + (name "seqwish-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$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 "seqwish-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs seqwish) + (append seqwish-x86-64-v2 + seqwish-x86-64-v3 + seqwish-x86-64-v4))) + (properties `((tunable? . #f))))) + (define-public smoothxg (package (name "smoothxg") @@ -2675,6 +2793,7 @@ Reference Consortium, HPRC} as a method to build a graph from the ;; Replace some packages with ones built targeting custom packages build ;; with glibc-hwcaps support. `(("sdsl-lite" . ,(const sdsl-lite-hwcaps)) + ("seqwish" . ,(const seqwish-hwcaps)) ("odgi" . ,(const odgi-hwcaps)) ("wfmash" . ,(const wfmash-hwcaps))))) |