diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2021-11-03 08:14:56 +0000 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-11-03 21:07:29 +0000 |
| commit | d54a4285ea92f899ad5a0309de9215447139fe5f (patch) | |
| tree | 4e27d3b22603984231e5b89011756dfa2ae1c8ea | |
| parent | 3c3d7f04100a1634ae5ea2b37a59e1cebcbbfdd2 (diff) | |
gnu: bedtools-2.18: Fix build with newer toolchain.
* 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.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 16 |
1 files changed, 14 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fbcd571c59..a731b9af06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -544,14 +544,26 @@ BED, GFF/GTF, VCF.") '(#:test-target "test" #: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) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (for-each (lambda (file) (install-file file bin)) - (find-files "bin" ".*"))) - #t))))))) + (find-files "bin" ".*")))))))) + (native-inputs + `(("python" ,python-wrapper))) + (inputs + `(("samtools" ,samtools) + ("zlib" ,zlib))))) (define-public pbbam (package |