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gnu: sra-tools: Fix glibc naming conflict.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase "patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
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@ -4832,7 +4832,19 @@ (define-public sra-tools
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(string-append "--with-ngs-sdk-prefix="
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(assoc-ref inputs "ngs-sdk"))
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(string-append "--with-hdf5-prefix="
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(assoc-ref inputs "hdf5")))))))))
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(assoc-ref inputs "hdf5"))))))
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;; This version of sra-tools fails to build with glibc because of a
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;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
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;; contains a definition of "canonicalize", so we rename it.
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;;
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;; See upstream bug report:
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;; https://github.com/ncbi/sra-tools/issues/67
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(add-after 'unpack 'patch-away-glibc-conflict
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(lambda _
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(substitute* "tools/bam-loader/bam.c"
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(("canonicalize\\(" line)
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(string-append "sra_tools_" line)))
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#t)))))
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(native-inputs `(("perl" ,perl)))
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(inputs
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`(("ngs-sdk" ,ngs-sdk)
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