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gnu: sra-tools: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3. [arguments]: Remove build phase patch-away-glibc-conflict.
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1 changed files with 2 additions and 14 deletions
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@ -5654,7 +5654,7 @@ (define-public python2-screed
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(define-public sra-tools
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(define-public sra-tools
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(package
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(package
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(name "sra-tools")
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(name "sra-tools")
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(version "2.8.2-1")
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(version "2.9.3")
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(source
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(source
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(origin
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(origin
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(method git-fetch)
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(method git-fetch)
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@ -5664,7 +5664,7 @@ (define-public sra-tools
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(file-name (git-file-name name version))
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(file-name (git-file-name name version))
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(sha256
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(sha256
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(base32
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(base32
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"12ln0pk8yajhmmj9xsfwa1qgv5m05ji40jsg17wdcls62zz6fwrk"))))
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"0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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`(#:parallel-build? #f ; not supported
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`(#:parallel-build? #f ; not supported
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@ -5733,18 +5733,6 @@ (define-public sra-tools
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(assoc-ref inputs "ngs-sdk"))
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(assoc-ref inputs "ngs-sdk"))
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(string-append "--with-hdf5-prefix="
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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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#t))
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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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#t)))))
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(native-inputs `(("perl" ,perl)))
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(native-inputs `(("perl" ,perl)))
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(inputs
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(inputs
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