gnu: ngless: Install links to required tools.
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools. [inputs]: Add prodigal, bwa, samtools, and minimap2.
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@ -14123,9 +14123,30 @@ absolute GSEA.")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'create-cabal-file
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(lambda _ (invoke "hpack") #t)))))
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(lambda _ (invoke "hpack") #t))
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;; These tools are expected to be installed alongside ngless.
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(add-after 'install 'link-tools
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
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(symlink (string-append (assoc-ref inputs "prodigal")
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"/bin/prodigal")
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(string-append bin "ngless-" ,version "-prodigal"))
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(symlink (string-append (assoc-ref inputs "minimap2")
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"/bin/minimap2")
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(string-append bin "ngless-" ,version "-minimap2"))
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(symlink (string-append (assoc-ref inputs "samtools")
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"/bin/samtools")
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(string-append bin "ngless-" ,version "-samtools"))
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(symlink (string-append (assoc-ref inputs "bwa")
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"/bin/bwa")
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(string-append bin "ngless-" ,version "-bwa"))
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#t))))))
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(inputs
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`(("ghc-aeson" ,ghc-aeson)
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`(("prodigal" ,prodigal)
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("bwa" ,bwa)
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("samtools" ,samtools)
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("minimap2" ,minimap2)
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("ghc-aeson" ,ghc-aeson)
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("ghc-ansi-terminal" ,ghc-ansi-terminal)
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("ghc-async" ,ghc-async)
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("ghc-atomic-write" ,ghc-atomic-write)
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