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gnu: Add cwltool.

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* gnu/packages/bioinformatics.scm (cwltool): New variable.
This commit is contained in:
Efraim Flashner 2020-11-23 15:14:01 +02:00
parent a78159547f
commit 964bc9e5fe
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1 changed files with 91 additions and 0 deletions
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91
gnu/packages/bioinformatics.scm
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@ -103,6 +103,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages node)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
#:use-module (gnu packages parallel)
@ -2618,6 +2619,96 @@ (define-public python-schema-salad
and record oriented data modeling and the Semantic Web.")
(license license:asl2.0)))
(define-public cwltool
(package
(name "cwltool")
(version "3.0.20201121085451")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/common-workflow-language/cwltool")
(commit version)))
(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") ; prov
((", < 3.5") "")) ; shellescape
#t))
(add-after 'unpack 'dont-use-git
(lambda _
(substitute* "gittaggers.py"
(("self.git_timestamp_tag\\(\\)")
(string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
(string-drop ,version 4) ")))")))
#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")
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
"def test_load_graph_fragment_from_packed")))
(substitute* "tests/test_examples.py"
(("def test_env_filtering")
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
"def test_env_filtering")))
;; Tries to use cwl-runners.
(substitute* "tests/test_examples.py"
(("def test_v1_0_arg_empty_prefix_separate_false")
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
"def test_v1_0_arg_empty_prefix_separate_false")))
#t)))))
(propagated-inputs
`(("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-shellescape" ,python-shellescape)
("python-typing-extensions" ,python-typing-extensions)
;; Not listed as needed but still necessary:
("node" ,node)))
(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
"This is the reference implementation of the @acronym{CWL, Common Workflow
Language} standards. The CWL open standards are for describing analysis
workflows and tools in a way that makes them portable and scalable across a
variety of software and hardware environments, from workstations to cluster,
cloud, and high performance computing (HPC) environments. CWL is designed to
meet the needs of data-intensive science, such as Bioinformatics, Medical
Imaging, Astronomy, Physics, and Chemistry. The @acronym{cwltool, CWL reference
implementation} is intended to be feature complete and to provide comprehensive
validation of CWL files as well as provide other tools related to working with
CWL descriptions.")
(license license:asl2.0)))
(define-public python-dendropy
(package
(name "python-dendropy")