aboutsummaryrefslogtreecommitdiff
path: root/gn/packages/cwl.scm
blob: 2642f906a197191569356b50dd19c56193e66f60 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
;; Experimental packaging for the Common Workflow Language (started by Bruno)

(define-module (gn packages cwl)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages check)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages rdf)
  #:use-module (gnu packages serialization)
  #:use-module (gn packages python)
  #:use-module (guix download)
  #:use-module (guix packages)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  ; #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  ; #:use-module (guix build-system trivial)
  #:use-module (srfi srfi-1))

(define-public cwltool ; guix: needs work
  (package
    (name "cwltool")
    (version "1.0.20181012180214")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
               "https://pypi.python.org/packages/source/c/cwltool/cwltool-"
               version
               ".tar.gz"))
        (sha256
          (base32
            "0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7"))))
    (build-system python-build-system)
    (inputs
     `(("python-bagit" ,python-bagit)
       ("python-setuptools" ,python-setuptools)
       ("python-pytest-cov" ,python-pytest-cov)
       ("python-prov" ,python-prov)
       ("python-pytest-runner" ,python-pytest-runner)
       ("python-rdflib" ,python-rdflib)
       ("python-typing-extensions" ,python-typing-extensions)
       ("python-pyparsing" ,python-pyparsing)
       ("python-subprocess32" ,python-subprocess32)
       ("python-ruamel.yaml" ,python-ruamel.yaml)
       ("python-cachecontrol" ,python-cachecontrol)
       ("python-mypy-extensions" ,python-mypy-extensions)
       ))
    (propagated-inputs
     `(("python-schema-salad" ,python-schema-salad)
       ("python-html5lib" ,python-html5lib)
       ))
    ; (arguments `(#:tests? #f)) ;; CWL includes no tests.
    (arguments
     `(;#:phases
       ; (modify-phases %standard-phases
       ;   (replace 'check
       ;     (lambda* (#:key inputs outputs #:allow-other-keys)
       ;       (invoke "python" "-m" "pytest")
       ;       )))
       #:tests? #f))   ; Disable for now

    (home-page
      "https://github.com/common-workflow-language/common-workflow-language")
    (synopsis
      "Common workflow language reference implementation")
    (description
      "Common workflow language reference implementation")
    (license license:asl2.0)))

(define-public python-schema-salad
  (package
    (name "python-schema-salad")
    (version "3.0.20181129082112")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "schema-salad" version))
        (sha256
          (base32
            "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97"))))
    (build-system python-build-system)
    (arguments `(#:tests? #f)) ;; CWL includes no tests.
    (inputs
      `(("python-cython" ,python-cython)
       ("python-setuptools" ,python-setuptools)
       ("python-rdflib-jsonld" ,python-rdflib-jsonld)
       ("python-mistune" ,python-mistune)))
    (propagated-inputs
     `(("python-rdflib" ,python-rdflib)
       ("python-avro" ,python-avro)
       ("python-pyyaml" ,python-pyyaml)
       ("python-requests" ,python-requests)
       ("python-shellescape" ,python-shellescape)
       ))
    (home-page
      "https://github.com/common-workflow-language/common-workflow-language")
    (synopsis
      "Schema Annotations for Linked Avro Data (SALAD)")
    (description
      "Schema Annotations for Linked Avro Data (SALAD)")
    (license license:asl2.0)))

(define-public python2-schema-salad
  (package-with-python2 python-schema-salad))