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-rw-r--r--gn/packages/bioinformatics.scm119
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)))))