diff options
Diffstat (limited to 'gn/packages/cwl.scm')
| -rw-r--r-- | gn/packages/cwl.scm | 115 |
1 files changed, 1 insertions, 114 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 9871ed9..a327187 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -1,124 +1,11 @@ (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)) + #:use-module (gnu packages bioinformatics)) -(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 |