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02/02: gnu: smithwaterman: Use new style for phases.
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guix-commits |
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Subject: |
02/02: gnu: smithwaterman: Use new style for phases. |
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Date: |
Mon, 4 Apr 2022 15:51:02 -0400 (EDT) |
efraim pushed a commit to branch master
in repository guix.
commit c1fc65ecb63b725ab770f20a3221be83f64dc68c
Author: Efraim Flashner <efraim@flashner.co.il>
AuthorDate: Mon Apr 4 22:45:37 2022 +0300
gnu: smithwaterman: Use new style for phases.
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
---
gnu/packages/bioinformatics.scm | 98 +++++++++++++++++++++--------------------
1 file changed, 50 insertions(+), 48 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b52fa1a61a..82d9a3eca6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14181,55 +14181,57 @@ some of the details of opening and jumping in
tabix-indexed files.")
(base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; There are no tests to run.
- #:make-flags (list (string-append "CXX=" ,(cxx-for-target))
- "libsw.a" "all")
+ (list
+ #:tests? #f ; There are no tests to run.
+ #:make-flags
+ #~(list (string-append "CXX=" #$(cxx-for-target))
+ "libsw.a" "all")
#:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- (add-after 'unpack 'patch-source
- (lambda _
- (substitute* "Makefile"
- (("-c ") "-c -fPIC "))
- ,@(if (%current-target-system)
- `((substitute* "Makefile"
- (("ld") (string-append ,(%current-target-system) "-ld"))
- (("ar") (string-append ,(%current-target-system)
"-ar"))))
- '())))
- (add-after 'build 'build-dynamic
- (lambda _
- (invoke ,(cxx-for-target)
- "-shared" "-o" "libsmithwaterman.so"
- "smithwaterman.o" "SmithWatermanGotoh.o"
- "disorder.o" "BandedSmithWaterman.o"
- "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin"))
- (lib (string-append out "/lib")))
- (install-file "smithwaterman" bin)
- (for-each
- (lambda (file)
- (install-file file (string-append out
"/include/smithwaterman")))
- (find-files "." "\\.h$"))
- (install-file "libsmithwaterman.so" lib)
- (install-file "libsw.a" lib)
- (mkdir-p (string-append lib "/pkgconfig"))
- (with-output-to-file (string-append lib
"/pkgconfig/smithwaterman.pc")
- (lambda _
- (format #t "prefix=~a~@
- exec_prefix=${prefix}~@
- libdir=${exec_prefix}/lib~@
- includedir=${prefix}/include/smithwaterman~@
- ~@
- ~@
- Name: smithwaterman~@
- Version: ~a~@
- Description: smith-waterman-gotoh alignment
algorithm~@
- Libs: -L${libdir} -lsmithwaterman~@
- Cflags: -I${includedir}~%"
- out ,version)))))))))
+ #~(modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "Makefile"
+ (("-c ") "-c -fPIC "))
+ #$@(if (%current-target-system)
+ #~((substitute* "Makefile"
+ (("ld") (string-append #$(%current-target-system)
"-ld"))
+ (("ar") (string-append #$(%current-target-system)
"-ar"))))
+ '())))
+ (add-after 'build 'build-dynamic
+ (lambda _
+ (invoke #$(cxx-for-target)
+ "-shared" "-o" "libsmithwaterman.so"
+ "smithwaterman.o" "SmithWatermanGotoh.o"
+ "disorder.o" "BandedSmithWaterman.o"
+ "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib")))
+ (install-file "smithwaterman" bin)
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out
"/include/smithwaterman")))
+ (find-files "." "\\.h$"))
+ (install-file "libsmithwaterman.so" lib)
+ (install-file "libsw.a" lib)
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib
"/pkgconfig/smithwaterman.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include/smithwaterman~@
+ ~@
+ ~@
+ Name: smithwaterman~@
+ Version: ~a~@
+ Description: smith-waterman-gotoh alignment
algorithm~@
+ Libs: -L${libdir} -lsmithwaterman~@
+ Cflags: -I${includedir}~%"
+ out #$version)))))))))
(home-page "https://github.com/ekg/smithwaterman";)
(synopsis "Implementation of the Smith-Waterman algorithm")
(description "Implementation of the Smith-Waterman algorithm.")