Package: guix-patches;
Reported by: Efraim Flashner <efraim <at> flashner.co.il>
Date: Sun, 29 Jan 2023 13:10:01 UTC
Severity: normal
Tags: patch
Done: Nicolas Goaziou <mail <at> nicolasgoaziou.fr>
Bug is archived. No further changes may be made.
Message #20 received at 61148 <at> debbugs.gnu.org (full text, mbox):
From: Efraim Flashner <efraim <at> flashner.co.il> To: 61148 <at> debbugs.gnu.org Cc: Efraim Flashner <efraim <at> flashner.co.il> Subject: [PATCH 5/5] gnu: vcflib: Update to 1.0.6. Date: Sun, 29 Jan 2023 15:12:38 +0200
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.6.
[source]: Adjust snippet to use unbundled wfa2-lib include directory.
Also unbundle simde, wfa2-lib. Remove googletest from unbundle list, it
is no longer in use.
[inputs]: Add curl, simde, wfa2-lib.
[native-inputs]: Add pybind11, pandoc when available. Add the sources
for libvcfh.
[arguments]: Adjust configure-flags to build without zig and to use the
unbundled wfa2-lib. Adjust custom 'build-shared-library phase for
changes in the source. Adjust custom 'unpack-submodule-sources for
changes in the source.
---
gnu/packages/bioinformatics.scm | 69 +++++++++++++++++++++++++--------
1 file changed, 52 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 05a07af7f3..c4eeb6d68f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16033,74 +16033,108 @@ (define-public fastahack
(define-public vcflib
(package
(name "vcflib")
- (version "1.0.3")
+ (version "1.0.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vcflib/vcflib")
- (commit (string-append "v" version))))
+ (commit (string-append "v" version))
+ (recursive? #t)))
(file-name (git-file-name name version))
(sha256
- (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh"))
+ (base32 "0zcs8j3vdajram53srvjmq353f3prqdbn8fvzja4412w4zay79fz"))
(modules '((guix build utils)))
(snippet
#~(begin
(substitute* "CMakeLists.txt"
((".*fastahack.*") "")
((".*smithwaterman.*") "")
+ ;; Also look for fastahack and smithwaterman since
+ ;; we've just unbundled them.
(("(pkg_check_modules\\(TABIXPP)" text)
(string-append
"pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
"pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
text))
+ ;; Also link vcflib to fastahack and smithwaterman.
(("\\$\\{TABIXPP_LIBRARIES\\}" text)
(string-append "${FASTAHACK_LIBRARIES} "
"${SMITHWATERMAN_LIBRARIES} "
- text)))
+ text))
+ ;; Honor setting WFA_INCLUDE_DIRS and not look at
+ ;; PREFIX/include/wfa2lib.
+ (((string-append "\\$\\{CMAKE_INSTALL_PREFIX\\}/"
+ "\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}/wfa2lib"))
+ "${WFA_INCLUDE_DIRS}"))
(substitute* (find-files "." "\\.(h|c)(pp)?$")
(("\"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"))))))
+ (substitute* "src/Variant.h"
+ (("wavefront/wfa.hpp") "wfa2lib/wavefront/wfa.hpp"))
+ (delete-file-recursively "src/simde")
+ (with-directory-excursion "contrib"
+ (for-each delete-file-recursively
+ '(;"c-progress-bar"
+ "fastahack"
+ "filevercmp"
+ "fsom"
+ "intervaltree"
+ "libVCFH"
+ "multichoose"
+ "smithwaterman"
+ "tabixpp"
+ "WFA2-lib")))))))
(build-system cmake-build-system)
(inputs
(list bzip2
+ curl
htslib
fastahack
perl
python
+ simde
smithwaterman
tabixpp
+ wfa2-lib
xz
zlib))
(native-inputs
`(("pkg-config" ,pkg-config)
+ ("pybind11" ,pybind11)
+ ,@(if (member (%current-system)
+ (package-transitive-supported-systems pandoc))
+ `(("pandoc" ,pandoc))
+ '())
;; Submodules.
- ;; This package builds against the .o files so we need to extract the source.
+ ;; Not all of these packages provide libraries to link against.
("filevercmp-src" ,(package-source filevercmp))
("fsom-src" ,(package-source fsom))
("intervaltree-src" ,(package-source intervaltree))
+ ("libvcfh-src" ,(package-source libvcfh))
("multichoose-src" ,(package-source multichoose))))
(arguments
(list #:configure-flags
- #~(list (string-append
+ #~(list "-DZIG=NO"
+ "-DWFA_GITMODULE=OFF"
+ (string-append "-DWFA_INCLUDE_DIRS="
+ (search-input-directory %build-inputs
+ "include/wfa2lib"))
+ "-DTABIX_FOUND=ON" ; Default to found
+ (string-append
"-DPKG_CONFIG_EXECUTABLE="
(search-input-file
%build-inputs (string-append
"/bin/" #$(pkg-config-for-target)))))
- #:tests? #f ; no tests
+ #:tests? #f ; Tests need more configuring.
#: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"))))
+ (("vcflib STATIC") "vcflib SHARED"))))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs native-inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
@@ -16114,10 +16148,11 @@ (define-public vcflib
source
"--strip-components=1")))))))
(and
- (unpack "filevercmp-src" "filevercmp")
- (unpack "fsom-src" "fsom")
- (unpack "intervaltree-src" "intervaltree")
- (unpack "multichoose-src" "multichoose")))))
+ (unpack "filevercmp-src" "contrib/filevercmp")
+ (unpack "fsom-src" "contrib/fsom")
+ (unpack "intervaltree-src" "contrib/intervaltree")
+ (unpack "libvcfh-src" "contrib/libvcfh")
+ (unpack "multichoose-src" "contrib/multichoose")))))
;; This pkg-config file is provided by other distributions.
(add-after 'install 'install-pkg-config-file
(lambda* (#:key outputs #:allow-other-keys)
--
Efraim Flashner <efraim <at> flashner.co.il> אפרים פלשנר
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