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
|
;; 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 node)
#:use-module (gnu packages rdf)
#:use-module (gnu packages serialization)
#:use-module (gnu packages time)
#:use-module (gnu packages version-control)
#: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
(let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727"))
(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"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/cwltool.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p"))))
(build-system python-build-system)
(propagated-inputs ; a lot of these are used for testing
`(("git" ,git)
("node" ,node)
("python-bagit" ,python-bagit)
("python-arcp" ,python-arcp)
("python-setuptools" ,python-setuptools)
("python-dateutil" ,python-dateutil)
("python-pytest-cov" ,python-pytest-cov)
("python-prov" ,python-prov)
("python-pytest-runner" ,python-pytest-runner)
("python-rdflib" ,python-rdflib)
("python-pyparsing" ,python-pyparsing)
("python-pytest-mock" ,python-pytest-mock)
("python-mock" ,python-mock)
("python-subprocess32" ,python-subprocess32)
("python-ruamel.yaml" ,python-ruamel.yaml)
("python-cachecontrol" ,python-cachecontrol)
("python-lxml" ,python-lxml)
("python-mypy-extensions" ,python-mypy-extensions)
("python-mistune" ,python-mistune)
("python-networkx" ,python-networkx)
("python-schema-salad" ,python-schema-salad)
("python-html5lib" ,python-html5lib)
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-typing-extensions" ,python-typing-extensions)
("python-scandir" ,python-scandir)
("python-psutil" ,python-psutil)
))
; (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))
|
