From: Arun Isaac <arunisaac@systemreboot.net>
To: 55125@debbugs.gnu.org
Cc: Arun Isaac <arunisaac@systemreboot.net>
Subject: [bug#55125] [PATCH 7/9] gnu: vcflib: Use G-expressions.
Date: Tue, 26 Apr 2022 18:16:37 +0530 [thread overview]
Message-ID: <20220426124639.17159-7-arunisaac@systemreboot.net> (raw)
In-Reply-To: <20220426124639.17159-1-arunisaac@systemreboot.net>
* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using
G-expressions.
[arguments]: Do not return #t from custom phases.
---
gnu/packages/bioinformatics.scm | 103 ++++++++++++++++----------------
1 file changed, 51 insertions(+), 52 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad69ca59cf..d74b8a0eb6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14548,27 +14548,27 @@ (define-public vcflib
(base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh"))
(modules '((guix build utils)))
(snippet
- '(begin
- (substitute* "CMakeLists.txt"
- ((".*fastahack.*") "")
- ((".*smithwaterman.*") "")
- (("(pkg_check_modules\\(TABIXPP)" text)
- (string-append
+ #~(begin
+ (substitute* "CMakeLists.txt"
+ ((".*fastahack.*") "")
+ ((".*smithwaterman.*") "")
+ (("(pkg_check_modules\\(TABIXPP)" text)
+ (string-append
"pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
"pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
text))
- (("\\$\\{TABIXPP_LIBRARIES\\}" text)
- (string-append "${FASTAHACK_LIBRARIES} "
- "${SMITHWATERMAN_LIBRARIES} "
- text)))
- (substitute* (find-files "." "\\.(h|c)(pp)?$")
- (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
- (("\"convert.h\"") "<smithwaterman/convert.h>")
- (("\"disorder.h\"") "<smithwaterman/disorder.h>")
- (("Fasta.h") "fastahack/Fasta.h"))
- (for-each delete-file-recursively
- '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
- "libVCFH" "multichoose" "smithwaterman"))))))
+ (("\\$\\{TABIXPP_LIBRARIES\\}" text)
+ (string-append "${FASTAHACK_LIBRARIES} "
+ "${SMITHWATERMAN_LIBRARIES} "
+ text)))
+ (substitute* (find-files "." "\\.(h|c)(pp)?$")
+ (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
+ (("\"convert.h\"") "<smithwaterman/convert.h>")
+ (("\"disorder.h\"") "<smithwaterman/disorder.h>")
+ (("Fasta.h") "fastahack/Fasta.h"))
+ (for-each delete-file-recursively
+ '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
+ "libVCFH" "multichoose" "smithwaterman"))))))
(build-system cmake-build-system)
(inputs
(list bzip2
@@ -14589,39 +14589,39 @@ (define-public vcflib
("intervaltree-src" ,(package-source intervaltree))
("multichoose-src" ,(package-source multichoose))))
(arguments
- `(#:tests? #f ; no tests
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'build-shared-library
- (lambda _
- (substitute* "CMakeLists.txt"
- (("vcflib STATIC") "vcflib SHARED"))
- (substitute* "test/Makefile"
- (("libvcflib.a") "libvcflib.so"))))
- (add-after 'unpack 'unpack-submodule-sources
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((unpack (lambda (source target)
- (mkdir target)
- (with-directory-excursion target
- (if (file-is-directory? (assoc-ref inputs source))
- (copy-recursively (assoc-ref inputs source) ".")
- (invoke "tar" "xvf"
- (assoc-ref inputs source)
- "--strip-components=1"))))))
- (and
- (unpack "filevercmp-src" "filevercmp")
- (unpack "fsom-src" "fsom")
- (unpack "intervaltree-src" "intervaltree")
- (unpack "multichoose-src" "multichoose")))))
- ;; This pkg-config file is provided by other distributions.
- (add-after 'install 'install-pkg-config-file
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (pkgconfig (string-append out "/lib/pkgconfig")))
- (mkdir-p pkgconfig)
- (with-output-to-file (string-append pkgconfig "/vcflib.pc")
+ (list #:tests? #f ; no tests
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'build-shared-library
(lambda _
- (format #t "prefix=~a~@
+ (substitute* "CMakeLists.txt"
+ (("vcflib STATIC") "vcflib SHARED"))
+ (substitute* "test/Makefile"
+ (("libvcflib.a") "libvcflib.so"))))
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (mkdir target)
+ (with-directory-excursion target
+ (if (file-is-directory? (assoc-ref inputs source))
+ (copy-recursively (assoc-ref inputs source) ".")
+ (invoke "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and
+ (unpack "filevercmp-src" "filevercmp")
+ (unpack "fsom-src" "fsom")
+ (unpack "intervaltree-src" "intervaltree")
+ (unpack "multichoose-src" "multichoose")))))
+ ;; This pkg-config file is provided by other distributions.
+ (add-after 'install 'install-pkg-config-file
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (pkgconfig (string-append out "/lib/pkgconfig")))
+ (mkdir-p pkgconfig)
+ (with-output-to-file (string-append pkgconfig "/vcflib.pc")
+ (lambda _
+ (format #t "prefix=~a~@
exec_prefix=${prefix}~@
libdir=${exec_prefix}/lib~@
includedir=${prefix}/include~@
@@ -14632,8 +14632,7 @@ (define-public vcflib
Description: C++ library for parsing and manipulating VCF files~@
Libs: -L${libdir} -lvcflib~@
Cflags: -I${includedir}~%"
- out ,version)))
- #t))))))
+ out #$version)))))))))
(home-page "https://github.com/vcflib/vcflib/")
(synopsis "Library for parsing and manipulating VCF files")
(description "Vcflib provides methods to manipulate and interpret
--
2.35.1
next prev parent reply other threads:[~2022-04-26 12:56 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-04-26 12:44 [bug#55125] [PATCH 0/9] Cross-compile vcflib for RISC-V Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 1/9] gnu: tabixpp: Use G-expressions Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 2/9] gnu: tabixpp: Use #:make-flags Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 3/9] gnu: tabixpp: Use build tools specific to the target Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 4/9] gnu: tabixpp: Add bzip2 and xz to inputs Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 5/9] gnu: fastahack: Use G-expressions Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 6/9] gnu: fastahack: Use compiler specific to the build target Arun Isaac
2022-04-26 12:46 ` Arun Isaac [this message]
2022-04-26 12:46 ` [bug#55125] [PATCH 8/9] gnu: vcflib: Find submodule sources in native-inputs during cross-compilation Arun Isaac
2022-04-26 12:46 ` [bug#55125] [PATCH 9/9] gnu: vcflib: Set absolute path to pkg-config Arun Isaac
2022-05-07 21:45 ` [bug#55125] [PATCH 0/9] Cross-compile vcflib for RISC-V Ludovic Courtès
2022-05-12 7:57 ` Arun Isaac
2022-05-09 8:31 ` bug#55125: " Efraim Flashner
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