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gnu: Remove pplacer-scripts.
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
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@ -13245,45 +13245,6 @@ (define-public adapterremoval
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sequence for paired-ended data, for which this information is not available.")
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sequence for paired-ended data, for which this information is not available.")
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(license license:gpl3+)))
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(license license:gpl3+)))
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;; This package is installed alongside 'pplacer'. It is a separate package so
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;; that it can use the python-build-system for the scripts that are
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;; distributed alongside the main OCaml binaries.
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(define pplacer-scripts
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(package
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(inherit pplacer)
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(name "pplacer-scripts")
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'enter-scripts-dir
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(lambda _ (chdir "scripts") #t))
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(replace 'check
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(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
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(add-after 'install 'wrap-executables
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin")))
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(let ((path (string-append
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(assoc-ref inputs "hmmer") "/bin:"
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(assoc-ref inputs "infernal") "/bin")))
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(display path)
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(wrap-program (string-append bin "/refpkg_align.py")
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`("PATH" ":" prefix (,path))))
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(let ((path (string-append
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(assoc-ref inputs "hmmer") "/bin")))
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(wrap-program (string-append bin "/hrefpkg_query.py")
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`("PATH" ":" prefix (,path)))))
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#t)))))
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(inputs
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`(("infernal" ,infernal)
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("hmmer" ,hmmer)))
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(propagated-inputs
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`(("python-biopython" ,python2-biopython)
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("taxtastic" ,taxtastic)))
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(synopsis "Pplacer Python scripts")))
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(define-public checkm
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(define-public checkm
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(package
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(package
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(name "checkm")
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(name "checkm")
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