mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2025-01-07 03:44:06 -05:00
gnu: vcflib: Update to 1.0.9.
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9. [source]: Update snippet. [inputs]: Add curl, pybind11, and wfa2-lib. [arguments]: Adjust and reformat.
This commit is contained in:
Ricardo Wurmus
parent
4ad51f5914
commit
2c09cc19e6
1 changed files with 71 additions and 60 deletions
|
|
@ -17170,16 +17170,16 @@ (define-public wfa2-lib
|
|||
(define-public vcflib
|
||||
(package
|
||||
(name "vcflib")
|
||||
(version "1.0.3")
|
||||
(version "1.0.9")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/vcflib/vcflib")
|
||||
(commit (string-append "v" version))))
|
||||
(url "https://github.com/vcflib/vcflib")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh"))
|
||||
(base32 "0cmznzq7hl5vr504ww262rwz5lfdfrca5ksbcvwh3cgp44fiwykv"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
#~(begin
|
||||
|
|
@ -17199,19 +17199,20 @@ (define-public vcflib
|
|||
(("\"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"))))))
|
||||
(("\"wavefront/wfa.hpp\"") "<wavefront/wfa.hpp>")
|
||||
(("Fasta.h") "fastahack/Fasta.h"))))))
|
||||
(build-system cmake-build-system)
|
||||
(inputs
|
||||
(list bzip2
|
||||
curl
|
||||
htslib
|
||||
fastahack
|
||||
perl
|
||||
python
|
||||
pybind11
|
||||
smithwaterman
|
||||
tabixpp
|
||||
wfa2-lib
|
||||
xz
|
||||
zlib))
|
||||
(native-inputs
|
||||
|
|
@ -17223,58 +17224,68 @@ (define-public vcflib
|
|||
("intervaltree-src" ,(package-source intervaltree))
|
||||
("multichoose-src" ,(package-source multichoose))))
|
||||
(arguments
|
||||
(list #:configure-flags
|
||||
#~(list (string-append
|
||||
"-DPKG_CONFIG_EXECUTABLE="
|
||||
(search-input-file
|
||||
%build-inputs (string-append
|
||||
"/bin/" #$(pkg-config-for-target)))))
|
||||
#:tests? #f ; no tests
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'build-shared-library
|
||||
(lambda _
|
||||
(substitute* "CMakeLists.txt"
|
||||
(("vcflib STATIC") "vcflib SHARED"))
|
||||
(substitute* "test/Makefile"
|
||||
(("libvcflib.a") "libvcflib.so"))))
|
||||
(add-after 'unpack 'unpack-submodule-sources
|
||||
(lambda* (#:key inputs native-inputs #:allow-other-keys)
|
||||
(let ((unpack (lambda (source target)
|
||||
(mkdir target)
|
||||
(with-directory-excursion target
|
||||
(let ((source (or (assoc-ref inputs source)
|
||||
(assoc-ref native-inputs source))))
|
||||
(if (file-is-directory? source)
|
||||
(copy-recursively source ".")
|
||||
(invoke "tar" "xvf"
|
||||
source
|
||||
"--strip-components=1")))))))
|
||||
(and
|
||||
(unpack "filevercmp-src" "filevercmp")
|
||||
(unpack "fsom-src" "fsom")
|
||||
(unpack "intervaltree-src" "intervaltree")
|
||||
(unpack "multichoose-src" "multichoose")))))
|
||||
;; This pkg-config file is provided by other distributions.
|
||||
(add-after 'install 'install-pkg-config-file
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(pkgconfig (string-append out "/lib/pkgconfig")))
|
||||
(mkdir-p pkgconfig)
|
||||
(with-output-to-file (string-append pkgconfig "/vcflib.pc")
|
||||
(lambda _
|
||||
(format #t "prefix=~a~@
|
||||
exec_prefix=${prefix}~@
|
||||
libdir=${exec_prefix}/lib~@
|
||||
includedir=${prefix}/include~@
|
||||
~@
|
||||
Name: vcflib~@
|
||||
Version: ~a~@
|
||||
Requires: smithwaterman, fastahack, tabixpp~@
|
||||
Description: C++ library for parsing and manipulating VCF files~@
|
||||
Libs: -L${libdir} -lvcflib~@
|
||||
Cflags: -I${includedir}~%"
|
||||
out #$version)))))))))
|
||||
(list
|
||||
#:configure-flags
|
||||
#~(list "-DZIG=OFF"
|
||||
"-DTABIXPP_LOCAL=OFF"
|
||||
"-DTABIX_FOUND=ON"
|
||||
"-DWFA_GITMODULE=OFF"
|
||||
"-DWFA_LINK_LIBRARIES=-lwfa2cpp"
|
||||
(string-append "-DPKG_CONFIG_EXECUTABLE="
|
||||
(search-input-file
|
||||
%build-inputs (string-append
|
||||
"/bin/" #$(pkg-config-for-target)))))
|
||||
#:tests? #f ; no tests
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'find-wf2lib-headers
|
||||
(lambda _
|
||||
(setenv "CPLUS_INCLUDE_PATH"
|
||||
(string-append
|
||||
#$(this-package-input "wfa2-lib")
|
||||
"/include/wfa2lib:"
|
||||
(or (getenv "CPLUS_INCLUDE_PATH") "")))))
|
||||
(add-after 'unpack 'build-shared-library
|
||||
(lambda _
|
||||
(substitute* "CMakeLists.txt"
|
||||
(("vcflib STATIC") "vcflib SHARED"))))
|
||||
(add-after 'unpack 'unpack-submodule-sources
|
||||
(lambda* (#:key inputs native-inputs #:allow-other-keys)
|
||||
(let ((unpack (lambda (source target)
|
||||
(mkdir-p target)
|
||||
(with-directory-excursion target
|
||||
(let ((source (or (assoc-ref inputs source)
|
||||
(assoc-ref native-inputs source))))
|
||||
(if (file-is-directory? source)
|
||||
(copy-recursively source ".")
|
||||
(invoke "tar" "xvf"
|
||||
source
|
||||
"--strip-components=1")))))))
|
||||
(and
|
||||
(unpack "filevercmp-src" "contrib/filevercmp")
|
||||
(unpack "fsom-src" "contrib/fsom")
|
||||
(unpack "intervaltree-src" "contrib/intervaltree")
|
||||
(unpack "multichoose-src" "contrib/multichoose")))))
|
||||
;; This pkg-config file is provided by other distributions.
|
||||
(add-after 'install 'install-pkg-config-file
|
||||
(lambda _
|
||||
(let ((pkgconfig (string-append #$output "/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=${prefix}/include~@
|
||||
~@
|
||||
Name: vcflib~@
|
||||
Version: ~a~@
|
||||
Requires: smithwaterman, fastahack, tabixpp~@
|
||||
Description: C++ library for parsing and manipulating VCF files~@
|
||||
Libs: -L${libdir} -lvcflib~@
|
||||
Cflags: -I${includedir}~%"
|
||||
#$output #$version)))))))))
|
||||
(home-page "https://github.com/vcflib/vcflib/")
|
||||
(synopsis "Library for parsing and manipulating VCF files")
|
||||
(description "Vcflib provides methods to manipulate and interpret
|
||||
|
|
|
|||
Loading…
Reference in a new issue