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gnu: Remove pplacer-scripts.

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* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
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Maxim Cournoyer 2022-05-31 14:19:59 -04:00
parent d397cb6207
commit ad030a0b7d
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1 changed files with 0 additions and 39 deletions
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gnu/packages/bioinformatics.scm
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@ -13245,45 +13245,6 @@ Additionally, the AdapterRemoval may be used to recover a consensus adapter
sequence for paired-ended data, for which this information is not available.")
(license license:gpl3+)))
;; This package is installed alongside 'pplacer'. It is a separate package so
;; that it can use the python-build-system for the scripts that are
;; distributed alongside the main OCaml binaries.
(define pplacer-scripts
(package
(inherit pplacer)
(name "pplacer-scripts")
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-scripts-dir
(lambda _ (chdir "scripts") #t))
(replace 'check
(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
(add-after 'install 'wrap-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(let ((path (string-append
(assoc-ref inputs "hmmer") "/bin:"
(assoc-ref inputs "infernal") "/bin")))
(display path)
(wrap-program (string-append bin "/refpkg_align.py")
`("PATH" ":" prefix (,path))))
(let ((path (string-append
(assoc-ref inputs "hmmer") "/bin")))
(wrap-program (string-append bin "/hrefpkg_query.py")
`("PATH" ":" prefix (,path)))))
#t)))))
(inputs
`(("infernal" ,infernal)
("hmmer" ,hmmer)))
(propagated-inputs
`(("python-biopython" ,python2-biopython)
("taxtastic" ,taxtastic)))
(synopsis "Pplacer Python scripts")))
(define-public checkm
(package
(name "checkm")