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gnu: ngless: Install links to required tools. 

* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
master
Ricardo Wurmus 2018-11-07 17:17:48 +01:00
parent fff67cc8a7
commit 21335fdbec
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1 changed files with 23 additions and 2 deletions
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gnu/packages/bioinformatics.scm
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@ -14123,9 +14123,30 @@ absolute GSEA.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'create-cabal-file
(lambda _ (invoke "hpack") #t)))))
(lambda _ (invoke "hpack") #t))
;; These tools are expected to be installed alongside ngless.
(add-after 'install 'link-tools
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(symlink (string-append (assoc-ref inputs "prodigal")
"/bin/prodigal")
(string-append bin "ngless-" ,version "-prodigal"))
(symlink (string-append (assoc-ref inputs "minimap2")
"/bin/minimap2")
(string-append bin "ngless-" ,version "-minimap2"))
(symlink (string-append (assoc-ref inputs "samtools")
"/bin/samtools")
(string-append bin "ngless-" ,version "-samtools"))
(symlink (string-append (assoc-ref inputs "bwa")
"/bin/bwa")
(string-append bin "ngless-" ,version "-bwa"))
#t))))))
(inputs
`(("ghc-aeson" ,ghc-aeson)
`(("prodigal" ,prodigal)
("bwa" ,bwa)
("samtools" ,samtools)
("minimap2" ,minimap2)
("ghc-aeson" ,ghc-aeson)
("ghc-ansi-terminal" ,ghc-ansi-terminal)
("ghc-async" ,ghc-async)
("ghc-atomic-write" ,ghc-atomic-write)