diff options
Diffstat (limited to 'gn/packages/cwl.scm')
| -rw-r--r-- | gn/packages/cwl.scm | 112 |
1 files changed, 0 insertions, 112 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm deleted file mode 100644 index fe5fcb2..0000000 --- a/gn/packages/cwl.scm +++ /dev/null @@ -1,112 +0,0 @@ -(define-module (gn packages cwl) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) - #:use-module (guix gexp) - #:use-module (guix packages) - #:use-module (guix build-system pyproject) - #:use-module (guix build-system python) - #:use-module (gnu packages) - #:use-module (gnu packages bioinformatics) - #:use-module (gnu packages docker) - #:use-module (gnu packages node) - #:use-module (gnu packages python-web) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages serialization) - #:use-module (gnu packages time) - #:use-module (gn packages python)) - - -(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 alternate entry point to allow cwl-runner -script as an implementation-agnostic script interpreter.") - (license license:asl2.0))) - -;; python-toil tightly integrates with cwltool using it as a library. So, -;; create a library version of cwltool where inputs become propagated inputs. -(define-public python-cwltool - (package - (inherit cwltool) - (name "python-cwltool") - (inputs - (list node)) - (propagated-inputs - (modify-inputs (package-inputs cwltool) - (delete "node"))))) - -(define-public python-toil - (package - (name "python-toil") - (version "6.1.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "toil" version)) - (sha256 - (base32 - "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'disable-optional-features - (lambda _ - (substitute* "requirements-cwl.txt" - ;; Loosen version restrictions on ruamel.yaml. - (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") - ;; Remove optional dependency on galaxy-util and - ;; galaxy-tool-util. TODO: Package these and restore these - ;; dependencies. - (("galaxy-util[^\n]*") "") - (("galaxy-tool-util[^\n]*") "")) - ;; Disable optional wdl, wes and mesos features. We don't yet - ;; have dependencies packaged for them. TODO: Package these - ;; dependencies and enable these features. - (substitute* "setup.py" - (("\"wdl\",") "") - (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") - "toil-cwl-runner = toil.cwl.cwltoil:main") - (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") - (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") - (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) - (propagated-inputs - (list python-addict - python-cachecontrol - python-configargparse - python-cwltool - python-dateutil - python-dill - python-docker - python-enlighten - python-psutil - python-pypubsub - python-pytz - python-pyyaml - python-requests - python-ruamel.yaml - python-typing-extensions-4.10 - python-urllib3)) - (home-page "https://github.com/DataBiosphere/toil") - (synopsis "Scalable, efficient and cross-platform workflow engine") - (description "Toil is a scalable, efficient, cross-platform pipeline -management system, written entirely in Python, and designed around the -principles of functional programming.") - (license (list license:asl2.0 ;; main license - license:expat)))) ;; src/toil/batchSystems/lsf.py and - ;; src/toil/batchSystems/lsfHelper.py |