TakeV/guix
1
0
Fork 0
Code Issues Pull requests Packages Projects Releases Wiki Activity

gnu: codingquarry: Use G-expression.

Browse source 
* gnu/packages/bioinformatics.scm (codingquarry)[arguments]: Use G-expression
to simplify 'install phase.  Install files to /share/codingquarry prefix.
[native-search-paths]: Adjust prefix.
[native-inputs]: Move python-2 from here...
[inputs]: ...to here.
This commit is contained in:
Ricardo Wurmus 2023-05-14 13:21:59 +02:00
parent 68ccd1a0d8
commit 7e303658d7
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 19 additions and 19 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

38
gnu/packages/bioinformatics.scm
View file

@ -3446,31 +3446,31 @@ (define-public codingquarry
"0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f ; no "check" target (list
#:phases #:tests? #f ;no "check" target
(modify-phases %standard-phases #:phases
(delete 'configure) #~(modify-phases %standard-phases
(replace 'install (delete 'configure)
(lambda* (#:key outputs #:allow-other-keys) (replace 'install
(let* ((out (assoc-ref outputs "out")) (lambda _
(bin (string-append out "/bin")) (let ((bin (string-append #$output "/bin"))
(doc (string-append out "/share/doc/codingquarry"))) (doc (string-append #$output "/share/doc/codingquarry")))
(install-file "INSTRUCTIONS.pdf" doc) (install-file "INSTRUCTIONS.pdf" doc)
(copy-recursively "QuarryFiles" (copy-recursively "QuarryFiles"
(string-append out "/QuarryFiles")) (string-append #$output
(install-file "CodingQuarry" bin) "/share/codingquarry/QuarryFiles"))
(install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) (install-file "CodingQuarry" bin)
#t))))) (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
(inputs (list openmpi)) ;; TODO: This package also needs a Python 2 variant of biopython
(inputs (list openmpi python-2)) ;Only Python 2 is supported
(native-search-paths (native-search-paths
(list (search-path-specification (list (search-path-specification
(variable "QUARRY_PATH") (variable "QUARRY_PATH")
(files '("QuarryFiles"))))) (files '("share/codingquarry/QuarryFiles")))))
(native-inputs `(("python" ,python-2))) ; Only Python 2 is supported (home-page "https://sourceforge.net/projects/codingquarry/")
(synopsis "Fungal gene predictor") (synopsis "Fungal gene predictor")
(description "CodingQuarry is a highly accurate, self-training GHMM fungal (description "CodingQuarry is a highly accurate, self-training GHMM fungal
gene predictor designed to work with assembled, aligned RNA-seq transcripts.") gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
(home-page "https://sourceforge.net/projects/codingquarry/")
(license license:gpl3+))) (license license:gpl3+)))
(define-public clustal-omega (define-public clustal-omega