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authorEfraim Flashner2020-07-19 04:30:22 -0500
committerEfraim Flashner2020-07-19 04:30:22 -0500
commit5d1c539797f973d624883057bac49c75a696c66b (patch)
tree628120577003dfc19514fedd3477a430eb0ecabf /gn/packages
parent632dfa25516ce98026cbad3e7b66ed4360b9e0c1 (diff)
downloadguix-bioinformatics-5d1c539797f973d624883057bac49c75a696c66b.tar.gz
gn: Add cwl-runner.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/cwl.scm38
1 files changed, 29 insertions, 9 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 938cbe3..2ee83d7 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -53,10 +53,7 @@
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false"))
#t)))))
(propagated-inputs
- `(;; does this need to be proagated?
- ("node" ,node)
-
- ("python-bagit" ,python-bagit)
+ `(("python-bagit" ,python-bagit)
("python-coloredlogs" ,python-coloredlogs)
("python-mypy-extensions" ,python-mypy-extensions)
("python-prov" ,python-prov)
@@ -67,15 +64,17 @@
("python-schema-salad" ,python-schema-salad-7)
("python-setuptools" ,python-setuptools)
("python-shellescape" ,python-shellescape)
- ("python-typing-extensions" ,python-typing-extensions)))
- (native-inputs
- `(("python-arcp" ,python-arcp)
+ ("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-humanfriendly" ,python-humanfriendly)
("python-lxml" ,python-lxml)
+ ("python-networkx" ,python-networkx)))
+ (native-inputs
+ `(("python-arcp" ,python-arcp)
+ ("python-humanfriendly" ,python-humanfriendly)
("python-mock" ,python-mock)
- ("python-networkx" ,python-networkx)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-mock" ,python-pytest-mock)
@@ -87,3 +86,24 @@
(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 reference implementation.")
+ (license license:asl2.0)))