diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 127 |
1 files changed, 127 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 71ea9c0..7a20200 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2058,6 +2058,18 @@ available to other researchers.") (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'use-gnuinstalldirs-macros + (lambda _ + (substitute* "CMakeLists.txt" + (("project\\(odgi\\)" all) + (string-append all "\ninclude(GNUInstallDirs)")) + ;; This is different than the default. + ;(("PUBLIC_HEADER DESTINATION include/odgi") + ; "PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}") + (("LIBRARY DESTINATION lib") + "LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}") + (("ARCHIVE DESTINATION lib") + "ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}")))) (add-after 'unpack 'link-to-libodgi (lambda _ ;; This lets us provide libraries for different psABI levels. @@ -2100,6 +2112,121 @@ in-memory footprint at the cost of packing and unpacking.") (properties '((tunable? . #t))) (license license:expat))) +(define-public odgi-x86-64-v2 + (package/inherit odgi + (name "odgi-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$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 #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public odgi-x86-64-v3 + (package/inherit odgi + (name "odgi-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$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 #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public odgi-x86-64-v4 + (package/inherit odgi + (name "odgi-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$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 #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +;; This copy of odgi will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public odgi-hwcaps + (package/inherit odgi + (name "odgi-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$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 "odgi-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs odgi) + (append odgi-x86-64-v2 + odgi-x86-64-v3 + odgi-x86-64-v4))) + (properties `((tunable? . #f))))) + (define-public vg (package (name "vg") |