gnu: Add intervaltree.
* gnu/packages/bioinformatics.scm (intervaltree): New variable. (vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.master
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@ -13384,6 +13384,36 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
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license:expat ;license for gffcompare
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license:expat ;license for gffcompare
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license:artistic2.0))))) ;license for gclib
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license:artistic2.0))))) ;license for gclib
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(define-public intervaltree
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(let ((commit "b90527f9e6d51cd36ecbb50429e4524d3a418ea5"))
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(package
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(name "intervaltree")
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(version (git-version "0.0.0" "1" commit))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/intervaltree/")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "0rgv6q5fl4x5d74n6p5wvdna6zmbdbqpb4jqqh6vq3670gn08xad"))))
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(build-system gnu-build-system)
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(arguments
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'(#:tests? #f ; No tests.
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#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
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"DESTDIR=\"\"")
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)))) ; There is no configure phase.
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(home-page "https://github.com/ekg/intervaltree")
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(synopsis "Minimal C++ interval tree implementation")
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(description "An interval tree can be used to efficiently find a set of
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numeric intervals overlapping or containing another interval. This library
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provides a basic implementation of an interval tree using C++ templates,
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allowing the insertion of arbitrary types into the tree.")
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(license license:expat))))
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(define-public python-intervaltree
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(define-public python-intervaltree
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(package
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(package
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(name "python-intervaltree")
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(name "python-intervaltree")
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@ -15086,15 +15116,7 @@ library automatically handles index file generation and use.")
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("fsom-src" ,(package-source fsom))
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("fsom-src" ,(package-source fsom))
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("filevercmp-src" ,(package-source filevercmp))
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("filevercmp-src" ,(package-source filevercmp))
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("fastahack-src" ,(package-source fastahack))
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("fastahack-src" ,(package-source fastahack))
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("intervaltree-src"
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("intervaltree-src" ,(package-source intervaltree))))
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,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/intervaltree/")
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(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
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(file-name "intervaltree-src-checkout")
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(sha256
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(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
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(arguments
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(arguments
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`(#:tests? #f ; no tests
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`(#:tests? #f ; no tests
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#:phases
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#:phases
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@ -15181,15 +15203,7 @@ manipulations on VCF files.")
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("fsom-src" ,(package-source fsom))
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("fsom-src" ,(package-source fsom))
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("filevercmp-src" ,(package-source filevercmp))
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("filevercmp-src" ,(package-source filevercmp))
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("fastahack-src" ,(package-source fastahack))
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("fastahack-src" ,(package-source fastahack))
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("intervaltree-src"
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("intervaltree-src" ,(package-source intervaltree))
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,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/intervaltree/")
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(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
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(file-name "intervaltree-src-checkout")
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(sha256
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(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
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;; These submodules are needed to run the tests.
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;; These submodules are needed to run the tests.
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("bash-tap-src" ,(package-source bash-tap))
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("bash-tap-src" ,(package-source bash-tap))
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("test-simple-bash-src"
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("test-simple-bash-src"
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