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spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.49 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=dEBZo8Fq; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 94DEF20D4E X-Spam-Score: 7.49 X-Migadu-Scanner: scn1.migadu.com X-TUID: x/Z5G2UdpokB * gnu/packages/bioinformatics.scm (tabixpp)[source]: Reindent. [arguments]: Use search-input-file and search-input-directory. [source, arguments]: Rewrite using G-expressions. Do not return #t from snippets and custom phases. --- gnu/packages/bioinformatics.scm | 80 ++++++++++++++++----------------- 1 file changed, 39 insertions(+), 41 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 40ccba247c..774da809d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14264,49 +14264,48 @@ (define-public tabixpp (name "tabixpp") (version "1.1.0") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/tabixpp") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) - (modules '((guix build utils))) - (snippet - `(begin - (delete-file-recursively "htslib") #t)))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) + (modules '((guix build utils))) + (snippet + #~(begin + (delete-file-recursively "htslib"))))) (build-system gnu-build-system) (inputs (list htslib zlib)) (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - ;; The build phase needs overriding the location of htslib. - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "INCLUDES= -I" htslib-ref "/include/htslib") - "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include")) - (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") - (invoke "ar" "rcs" "libtabixpp.a" "tabix.o")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (bin (string-append out "/bin"))) - (install-file "tabix++" bin) - (install-file "libtabixpp.so" lib) - (install-file "libtabixpp.a" lib) - (install-file "tabix.hpp" (string-append out "/include")) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") - (lambda _ - (format #t "prefix=~a~@ + (list #:tests? #f ; There are no tests to run. + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; The build phase needs overriding the location of htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (invoke "make" + (string-append "HTS_LIB=" (search-input-file inputs "/lib/libhts.a")) + (string-append "INCLUDES= -I" (search-input-directory inputs "/include/htslib")) + "HTS_HEADERS=" ; No need to check for headers here. + (string-append "LIBPATH=-L. -L" (search-input-directory inputs "/include"))) + (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") + (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (install-file "tabix++" bin) + (install-file "libtabixpp.so" lib) + (install-file "libtabixpp.a" lib) + (install-file "tabix.hpp" (string-append out "/include")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14317,8 +14316,7 @@ (define-public tabixpp Description: C++ wrapper around tabix project~@ Libs: -L${libdir} -ltabixpp~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (home-page "https://github.com/ekg/tabixpp") (synopsis "C++ wrapper around tabix project") (description "This is a C++ wrapper around the Tabix project which abstracts -- 2.35.1