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authorEfraim Flashner2023-09-26 10:37:16 +0300
committerEfraim Flashner2023-09-26 10:37:16 +0300
commit6ee7dfd989d93a083b13a0463e486b5c85ca1ac9 (patch)
tree857302d48a7e8383e30bc2a08262cf8eaec27a31 /gn/packages
parent3eb44711f16cd57ce625ce1011041390c7c270da (diff)
downloadguix-bioinformatics-6ee7dfd989d93a083b13a0463e486b5c85ca1ac9.tar.gz
seqwish: Build and link against shared library.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm32
1 files changed, 21 insertions, 11 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 285b01d..50c207d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1609,7 +1609,8 @@ runApp(launch.browser=0, port=4208)~%\n"
(file-name (git-file-name name version))
(sha256
(base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x"))
- (patches (search-patches "seqwish-paryfor-riscv.diff"))
+ (patches (search-patches "seqwish-paryfor-riscv.diff"
+ "seqwish-shared-library.diff"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ -1626,14 +1627,24 @@ runApp(launch.browser=0, port=4208)~%\n"
(build-system cmake-build-system)
(arguments
`(#:configure-flags
- '(,@(if (target-x86?)
- ;; This is the minimum needed to compile on x86_64, and is a
- ;; subset of any other optimizations which might be applied.
- '("-DCMAKE_C_FLAGS=-mcx16"
- "-DCMAKE_CXX_FLAGS=-mcx16")
- '()))
+ (cons* ,@(if (target-x86?)
+ ;; This is the minimum needed to compile on x86_64, and is a
+ ;; subset of any other optimizations which might be applied.
+ '("-DCMAKE_C_FLAGS=-mcx16"
+ "-DCMAKE_CXX_FLAGS=-mcx16")
+ '())
+ '("-DSEQWISH_LINK_SHARED_LIBRARY=ON"))
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ ;; This stashes the build version in the executable.
+ (mkdir "include")
+ (substitute* "CMakeLists.txt"
+ (("^execute_process") "#execute_process"))
+ (with-output-to-file "include/seqwish_git_version.hpp"
+ (lambda ()
+ (format #t "#define SEQWISH_GIT_VERSION \"~a\"~%" ,version)))))
(add-after 'unpack 'link-with-some-shared-libraries
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("CMakeLists.txt"
@@ -1642,11 +1653,10 @@ runApp(launch.browser=0, port=4208)~%\n"
(("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"")
(("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"")
(("\\$\\{sdsl-lite_INCLUDE\\}")
- (string-append (assoc-ref inputs "sdsl-lite")
- "/include/sdsl"))
+ (search-input-directory inputs "/include/sdsl"))
(("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}")
- (string-append (assoc-ref inputs "libdivsufsort")
- "/include")))))
+ (dirname
+ (search-input-file inputs "/include/divsufsort.h"))))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
;; Add seqwish to the PATH for the tests.