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authorRicardo Wurmus <rekado@elephly.net>2021-11-03 08:14:56 +0000
committerRicardo Wurmus <rekado@elephly.net>2021-11-03 21:07:29 +0000
commitd54a4285ea92f899ad5a0309de9215447139fe5f (patch)
tree4e27d3b22603984231e5b89011756dfa2ae1c8ea /gnu/packages/bioinformatics.scm
parent3c3d7f04100a1634ae5ea2b37a59e1cebcbbfdd2 (diff)
downloadguix-d54a4285ea92f899ad5a0309de9215447139fe5f.tar.gz
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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm16
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