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
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
|
(define-module (gn packages cwl)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gn packages python)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages check)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages node)
#:use-module (gnu packages rdf)
#:use-module (gnu packages serialization)
#:use-module (gnu packages time)
#:use-module (gnu packages version-control)
#:use-module (gnu packages xml))
(define-public python-pydot ;; can be updated in GNU Guix - this is a copy
(package
(name "python-pydot")
(version "1.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pydot" version))
(sha256
(base32
"00az4cbf8bv447lkk9xi6pjm7gcc7ia33y4pm71fwfwis56rv76l"))))
(build-system python-build-system)
(native-inputs
;; For tests.
`(("python-chardet" ,python-chardet)))
(propagated-inputs
`(("python-pyparsing" ,python-pyparsing)))
(home-page "https://github.com/erocarrera/pydot")
(synopsis "Python interface to Graphviz's DOT language")
(description
"Pydot provides an interface to create, handle, modify and process
graphs in Graphviz's DOT language, written in pure Python.")
(license license:expat)))
(define-public cwltool
(let ((commit "78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf")
(revision "1"))
(package
(name "cwltool")
(version "3.0.20201117141248")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/common-workflow-language/cwltool.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'loosen-version-restrictions
(lambda _
(substitute* "setup.py"
(("== 1.5.1") ">=1.5.1"))
#t))
(add-after 'unpack 'modify-tests
(lambda _
;; Tries to connect to the internet.
(delete-file "tests/test_udocker.py")
(delete-file "tests/test_http_input.py")
(substitute* "tests/test_load_tool.py"
(("def test_load_graph_fragment_from_packed")
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed"))
(substitute* "tests/test_examples.py"
(("def test_env_filtering")
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_env_filtering"))
;; Tries to use cwl-runners.
(substitute* "tests/test_examples.py"
(("def test_v1_0_arg_empty_prefix_separate_false")
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false"))
#t)))))
(propagated-inputs
`(("git" ,git)
("python-argcomplete" ,python-argcomplete)
("python-bagit" ,python-bagit)
("python-coloredlogs" ,python-coloredlogs)
("python-mypy-extensions" ,python-mypy-extensions)
("python-prov" ,python-prov)
("python-pydot" ,python-pydot)
("python-psutil" ,python-psutil)
("python-rdflib" ,python-rdflib)
("python-requests" ,python-requests)
("python-ruamel.yaml" ,python-ruamel.yaml)
("python-schema-salad" ,python-schema-salad)
("python-setuptools" ,python-setuptools)
("python-shellescape" ,python-shellescape)
("python-typing-extensions" ,python-typing-extensions)
;; Not listed as needed but seems to be necessary:
("node" ,node)
("python-cachecontrol" ,python-cachecontrol-0.11)
("python-dateutil" ,python-dateutil)
("python-lxml" ,python-lxml)
("python-networkx" ,python-networkx)))
(native-inputs
`(("python-arcp" ,python-arcp)
("python-humanfriendly" ,python-humanfriendly)
("python-mock" ,python-mock)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-mock" ,python-pytest-mock)
("python-pytest-runner" ,python-pytest-runner)
("python-rdflib-jsonld" ,python-rdflib-jsonld)))
(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 cwl-runner
(package
(name "cwl-runner")
(version "1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cwl_runner" version))
(sha256
(base32
"0011am2xqwchysdznayrmwhg4bfjl4wlq6m4k20z1m7gccyzjgw0"))))
(build-system python-build-system)
(propagated-inputs
`(("cwltool" ,cwltool)))
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis "Common workflow language reference implementation")
(description
"Common workflow language alternate entry point to allow cwl-runner
script as an implementation-agnostic script interpreter.")
(license license:asl2.0)))
|
