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gnu: smithwaterman: Use new style for phases.

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* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
This commit is contained in:
Efraim Flashner 2022-04-04 22:45:37 +03:00
parent 855c8d9d41
commit c1fc65ecb6
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1 changed files with 50 additions and 48 deletions
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@ -14181,55 +14181,57 @@ some of the details of opening and jumping in tabix-indexed files.")
(base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs")))) (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; There are no tests to run. (list
#:make-flags (list (string-append "CXX=" ,(cxx-for-target)) #:tests? #f ; There are no tests to run.
"libsw.a" "all") #:make-flags
#~(list (string-append "CXX=" #$(cxx-for-target))
"libsw.a" "all")
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase. (delete 'configure) ; There is no configure phase.
(add-after 'unpack 'patch-source (add-after 'unpack 'patch-source
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
(("-c ") "-c -fPIC ")) (("-c ") "-c -fPIC "))
,@(if (%current-target-system) #$@(if (%current-target-system)
`((substitute* "Makefile" #~((substitute* "Makefile"
(("ld") (string-append ,(%current-target-system) "-ld")) (("ld") (string-append #$(%current-target-system) "-ld"))
(("ar") (string-append ,(%current-target-system) "-ar")))) (("ar") (string-append #$(%current-target-system) "-ar"))))
'()))) '())))
(add-after 'build 'build-dynamic (add-after 'build 'build-dynamic
(lambda _ (lambda _
(invoke ,(cxx-for-target) (invoke #$(cxx-for-target)
"-shared" "-o" "libsmithwaterman.so" "-shared" "-o" "libsmithwaterman.so"
"smithwaterman.o" "SmithWatermanGotoh.o" "smithwaterman.o" "SmithWatermanGotoh.o"
"disorder.o" "BandedSmithWaterman.o" "disorder.o" "BandedSmithWaterman.o"
"LeftAlign.o" "Repeats.o" "IndelAllele.o"))) "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")) (bin (string-append out "/bin"))
(lib (string-append out "/lib"))) (lib (string-append out "/lib")))
(install-file "smithwaterman" bin) (install-file "smithwaterman" bin)
(for-each (for-each
(lambda (file) (lambda (file)
(install-file file (string-append out "/include/smithwaterman"))) (install-file file (string-append out "/include/smithwaterman")))
(find-files "." "\\.h$")) (find-files "." "\\.h$"))
(install-file "libsmithwaterman.so" lib) (install-file "libsmithwaterman.so" lib)
(install-file "libsw.a" lib) (install-file "libsw.a" lib)
(mkdir-p (string-append lib "/pkgconfig")) (mkdir-p (string-append lib "/pkgconfig"))
(with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc")
(lambda _ (lambda _
(format #t "prefix=~a~@ (format #t "prefix=~a~@
exec_prefix=${prefix}~@ exec_prefix=${prefix}~@
libdir=${exec_prefix}/lib~@ libdir=${exec_prefix}/lib~@
includedir=${prefix}/include/smithwaterman~@ includedir=${prefix}/include/smithwaterman~@
~@ ~@
~@ ~@
Name: smithwaterman~@ Name: smithwaterman~@
Version: ~a~@ Version: ~a~@
Description: smith-waterman-gotoh alignment algorithm~@ Description: smith-waterman-gotoh alignment algorithm~@
Libs: -L${libdir} -lsmithwaterman~@ Libs: -L${libdir} -lsmithwaterman~@
Cflags: -I${includedir}~%" Cflags: -I${includedir}~%"
out ,version))))))))) out #$version)))))))))
(home-page "https://github.com/ekg/smithwaterman") (home-page "https://github.com/ekg/smithwaterman")
(synopsis "Implementation of the Smith-Waterman algorithm") (synopsis "Implementation of the Smith-Waterman algorithm")
(description "Implementation of the Smith-Waterman algorithm.") (description "Implementation of the Smith-Waterman algorithm.")