Merge branch 'master' of /home/git/public/guix-bioinformatics

1 files changed, 117 insertions, 0 deletions

diff --git a/gn/packages/datastructures.scm b/gn/packages/datastructures.scm
new file mode 100644
index 0000000..1744420
--- /dev/null
+++ b/gn/packages/datastructures.scm
@@ -0,0 +1,117 @@
+;; Datastructures module
+
+(define-module (gn packages datastructures)
+  #:use-module (guix packages)
+  #:use-module (guix gexp)
+  #:use-module (guix utils)
+  #:use-module (gnu packages datastructures))
+
+(define sdsl-lite-x86-64-v2
+  (package/inherit sdsl-lite
+    (name "sdsl-lite-x86-64-v2")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sdsl-lite)
+       ((#:configure-flags flags #~'())
+        #~(append (list "-DCMAKE_CXX_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 "/include"))))
+            (replace 'install-static-library
+              (lambda* (#:key outputs #:allow-other-keys)
+                (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libsdsl.a"))
+                  (mkdir-p (dirname (string-append #$output:static lib)))
+                  (copy-file "lib/libsdsl_static.a"
+                             (string-append #$output:static lib)))))))))
+    (supported-systems '("x86_64-linux"))
+    (properties `((hidden? . #t)))))
+
+(define sdsl-lite-x86-64-v3
+  (package/inherit sdsl-lite
+    (name "sdsl-lite-x86-64-v3")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sdsl-lite)
+       ((#:configure-flags flags #~'())
+        #~(append (list "-DCMAKE_CXX_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 "/include"))))
+            (replace 'install-static-library
+              (lambda* (#:key outputs #:allow-other-keys)
+                (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libsdsl.a"))
+                  (mkdir-p (dirname (string-append #$output:static lib)))
+                  (copy-file "lib/libsdsl_static.a"
+                             (string-append #$output:static lib)))))))))
+    (supported-systems '("x86_64-linux"))
+    (properties `((hidden? . #t)))))
+
+(define sdsl-lite-x86-64-v4
+  (package/inherit sdsl-lite
+    (name "sdsl-lite-x86-64-v4")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sdsl-lite)
+       ((#:configure-flags flags #~'())
+        #~(append (list "-DCMAKE_CXX_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 "/include"))))
+            (replace 'install-static-library
+              (lambda* (#:key outputs #:allow-other-keys)
+                (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libsdsl.a"))
+                  (mkdir-p (dirname (string-append #$output:static lib)))
+                  (copy-file "lib/libsdsl_static.a"
+                             (string-append #$output:static lib)))))))))
+    (supported-systems '("x86_64-linux"))
+    (properties `((hidden? . #t)))))
+
+(define-public sdsl-lite-hwcaps
+  (package/inherit sdsl-lite
+    (name "sdsl-lite-hwcaps")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sdsl-lite)
+       ((#:phases phases #~%standard-phases)
+        #~(modify-phases #$phases
+            (add-after 'install 'install-optimized-libraries
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                (let ((hwcaps "/lib/glibc-hwcaps"))
+                  (copy-recursively
+                    (string-append (assoc-ref inputs "sdsl-lite-x86-64-v2")
+                                   hwcaps "/x86-64-v2")
+                    (string-append #$output hwcaps "/x86-64-v2"))
+                  (copy-recursively
+                    (string-append (assoc-ref inputs "sdsl-lite-x86-64-v3")
+                                   hwcaps "/x86-64-v3")
+                    (string-append #$output hwcaps "/x86-64-v3"))
+                  (copy-recursively
+                    (string-append (assoc-ref inputs "sdsl-lite-x86-64-v4")
+                                   hwcaps "/x86-64-v4")
+                    (string-append #$output hwcaps "/x86-64-v4")))))))))
+    (native-inputs
+     (modify-inputs (package-native-inputs sdsl-lite)
+                    (append sdsl-lite-x86-64-v2
+                            sdsl-lite-x86-64-v3
+                            sdsl-lite-x86-64-v4)))
+    (properties `((tunable? . #f)))))