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gnu: vcflib: Fix generated pkg-config file.

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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
This commit is contained in:
Efraim Flashner 2021-02-01 18:18:42 +02:00
parent 15078567c1
commit 877ab0266c
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GPG key ID: 41AAE7DCCA3D8351
2 changed files with 5 additions and 5 deletions
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8
gnu/packages/bioinformatics.scm
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@ -15209,18 +15209,18 @@ library automatically handles index file generation and use.")
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
(pkgconfig (string-append out "/lib/pkgconfig"))) (pkgconfig (string-append out "/lib/pkgconfig")))
(mkdir-p pkgconfig) (mkdir-p pkgconfig)
(with-output-to-file (string-append pkgconfig "/libvcflib.pc") (with-output-to-file (string-append pkgconfig "/vcflib.pc")
(lambda _ (lambda _
(format #t "prefix=~a~@ (format #t "prefix=~a~@
exec_prefix=${prefix}~@ exec_prefix=${prefix}~@
libdir=${exec_prefix}/lib~@ libdir=${exec_prefix}/lib~@
includedir=${prefix}/include~@ includedir=${prefix}/include~@
~@ ~@
Name: libvcflib~@ Name: vcflib~@
Version: ~a~@ Version: ~a~@
Requires: smithwaterman, fastahack~@ Requires: smithwaterman, fastahack, tabixpp~@
Description: C++ library for parsing and manipulating VCF files~@ Description: C++ library for parsing and manipulating VCF files~@
Libs: -L${libdir} -llibvcflib~@ Libs: -L${libdir} -lvcflib~@
Cflags: -I${includedir}~%" Cflags: -I${includedir}~%"
out ,version))) out ,version)))
#t)))))) #t))))))

2
gnu/packages/patches/freebayes-devendor-deps.patch
View file

@ -23,7 +23,7 @@ index f6bf242..bded4af 100644
+tabixpp_dep = dependency('tabixpp', required : false) +tabixpp_dep = dependency('tabixpp', required : false)
+fastahack_dep = dependency('fastahack', required : false) +fastahack_dep = dependency('fastahack', required : false)
+smithwaterman_dep = dependency('smithwaterman', required : false) +smithwaterman_dep = dependency('smithwaterman', required : false)
+vcflib_dep = dependency('libvcflib', required: false) +vcflib_dep = dependency('vcflib', required: false)
thread_dep = dependency('threads') thread_dep = dependency('threads')
if htslib_dep.found() if htslib_dep.found()