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gnu: bedtools-2.18: Fix build with newer toolchain.

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* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase
'compatibility, fixing syntax quirks that are problematic with newer
toolchains.
[native-inputs]: Do not inherit.
[inherit]: Do not inherit.
This commit is contained in:
Ricardo Wurmus 2021-11-03 08:14:56 +00:00
parent 3c3d7f0410
commit d54a4285ea
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GPG key ID: 197A5888235FACAC
1 changed files with 14 additions and 2 deletions
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gnu/packages/bioinformatics.scm
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@ -544,14 +544,26 @@ (define-public bedtools-2.18
'(#:test-target "test" '(#:test-target "test"
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'compatibility
(lambda _
(substitute* "src/utils/fileType/FileRecordTypeChecker.h"
(("static const float PERCENTAGE")
"static constexpr float PERCENTAGE"))
(substitute* "src/utils/general/DualQueue.h"
(("template <class T, template<class T> class CompareFunc>")
"template <class T, template<class U> class CompareFunc>"))))
(delete 'configure) (delete 'configure)
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file) (for-each (lambda (file)
(install-file file bin)) (install-file file bin))
(find-files "bin" ".*"))) (find-files "bin" ".*"))))))))
#t))))))) (native-inputs
`(("python" ,python-wrapper)))
(inputs
`(("samtools" ,samtools)
("zlib" ,zlib)))))
(define-public pbbam (define-public pbbam
(package (package