gnu: Add cwltool.
* gnu/packages/bioinformatics.scm (cwltool): New variable.
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@ -103,6 +103,7 @@ (define-module (gnu packages bioinformatics)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages node)
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#:use-module (gnu packages ocaml)
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#:use-module (gnu packages pcre)
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#:use-module (gnu packages parallel)
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@ -2618,6 +2619,96 @@ (define-public python-schema-salad
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and record oriented data modeling and the Semantic Web.")
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(license license:asl2.0)))
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(define-public cwltool
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(package
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(name "cwltool")
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(version "3.0.20201121085451")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/common-workflow-language/cwltool")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'loosen-version-restrictions
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(lambda _
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(substitute* "setup.py"
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(("== 1.5.1") ">=1.5.1") ; prov
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((", < 3.5") "")) ; shellescape
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#t))
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(add-after 'unpack 'dont-use-git
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(lambda _
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(substitute* "gittaggers.py"
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(("self.git_timestamp_tag\\(\\)")
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(string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
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(string-drop ,version 4) ")))")))
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#t))
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(add-after 'unpack 'modify-tests
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(lambda _
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;; Tries to connect to the internet.
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(delete-file "tests/test_udocker.py")
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(delete-file "tests/test_http_input.py")
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(substitute* "tests/test_load_tool.py"
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(("def test_load_graph_fragment_from_packed")
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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"def test_load_graph_fragment_from_packed")))
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(substitute* "tests/test_examples.py"
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(("def test_env_filtering")
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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"def test_env_filtering")))
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;; Tries to use cwl-runners.
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(substitute* "tests/test_examples.py"
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(("def test_v1_0_arg_empty_prefix_separate_false")
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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"def test_v1_0_arg_empty_prefix_separate_false")))
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#t)))))
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(propagated-inputs
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`(("python-argcomplete" ,python-argcomplete)
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("python-bagit" ,python-bagit)
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("python-coloredlogs" ,python-coloredlogs)
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("python-mypy-extensions" ,python-mypy-extensions)
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("python-prov" ,python-prov)
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("python-pydot" ,python-pydot)
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("python-psutil" ,python-psutil)
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("python-rdflib" ,python-rdflib)
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("python-requests" ,python-requests)
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("python-ruamel.yaml" ,python-ruamel.yaml)
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("python-schema-salad" ,python-schema-salad)
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("python-shellescape" ,python-shellescape)
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("python-typing-extensions" ,python-typing-extensions)
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;; Not listed as needed but still necessary:
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("node" ,node)))
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(native-inputs
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`(("python-arcp" ,python-arcp)
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("python-humanfriendly" ,python-humanfriendly)
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("python-mock" ,python-mock)
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("python-pytest" ,python-pytest)
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("python-pytest-cov" ,python-pytest-cov)
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("python-pytest-mock" ,python-pytest-mock)
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("python-pytest-runner" ,python-pytest-runner)
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("python-rdflib-jsonld" ,python-rdflib-jsonld)))
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(home-page
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"https://github.com/common-workflow-language/common-workflow-language")
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(synopsis "Common Workflow Language reference implementation")
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(description
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"This is the reference implementation of the @acronym{CWL, Common Workflow
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Language} standards. The CWL open standards are for describing analysis
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workflows and tools in a way that makes them portable and scalable across a
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variety of software and hardware environments, from workstations to cluster,
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cloud, and high performance computing (HPC) environments. CWL is designed to
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meet the needs of data-intensive science, such as Bioinformatics, Medical
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Imaging, Astronomy, Physics, and Chemistry. The @acronym{cwltool, CWL reference
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implementation} is intended to be feature complete and to provide comprehensive
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validation of CWL files as well as provide other tools related to working with
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CWL descriptions.")
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(license license:asl2.0)))
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(define-public python-dendropy
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(package
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(name "python-dendropy")
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