upstream cwltools and dependant packages

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