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authorArun Isaac <arunisaac@systemreboot.net>2022-04-26 18:16:31 +0530
committerEfraim Flashner <efraim@flashner.co.il>2022-05-09 11:13:40 +0300
commitff1fd3b0120317adae839ca28658eddc480f130c (patch)
tree826a91c7f5162c744cfd1113bebe9f3d126a7632 /gnu/packages/bioinformatics.scm
parent9017c2406b1c1a0cb9f393fd09459db1d06caba9 (diff)
gnu: tabixpp: Use G-expressions.
* 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. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm80
1 files changed, 39 insertions, 41 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ae35087964..ed4836998b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14283,49 +14283,48 @@ mutations from scRNA-Seq data.")
(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=${prefix}/include~@
@@ -14336,8 +14335,7 @@ mutations from scRNA-Seq data.")
Description: C++ wrapper around tabix project~@
Libs: -L${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