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-rw-r--r--gn/packages/bioinformatics.scm75
-rw-r--r--gn/packages/cwl.scm77
-rw-r--r--gn/packages/python.scm75
3 files changed, 76 insertions, 151 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5a33929..02ac1e8 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1266,78 +1266,3 @@ COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use
it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely
available to other researchers.")
(license license:asl2.0))))
-
-(define-public python-arvados-python-client
- (package
- (name "python-arvados-python-client")
- (version "2.0.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "arvados-python-client" version))
- (sha256
- (base32
- "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f)) ; tests not included?
- (propagated-inputs
- `(("python-ciso8601" ,python-ciso8601)
- ("python-future" ,python-future)
- ;("python-google-api-python-client" ,python-google-api-python-client)
- ("python-google-api-client" ,python-google-api-client)
- ("python-httplib2" ,python-httplib2)
- ("python-pycurl" ,python-pycurl)
- ("python-ruamel.yaml" ,python-ruamel.yaml-0.15)
- ("python-setuptools" ,python-setuptools)
- ("python-ws4py" ,python-ws4py)))
- (native-inputs
- `(("python-mock" ,python-mock)
- ("python-oauth2client" ,python-oauth2client)
- ("python-pbr" ,python-pbr-1.6.0)
- ("python-pyyaml" ,python-pyyaml)
- ("python-uritemplate" ,python-uritemplate)))
- (home-page "https://arvados.org")
- (synopsis "Arvados client library")
- (description "This package provides the arvados module, an API client for
-Arvados. It also includes higher-level functions to help you write Crunch
-scripts, and command-line tools to store and retrieve data in the Keep storage
-server.")
- (license license:asl2.0)))
-
-(define-public python-schema-salad
- (package
- (name "python-schema-salad")
- (version "5.0.20200416112825")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "schema-salad" version))
- (sha256
- (base32
- "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz"))))
- (build-system python-build-system)
- (propagated-inputs
- `(("python-cachecontrol" ,python-cachecontrol-0.11)
- ("python-lockfile" ,python-lockfile)
- ("python-mistune" ,python-mistune)
- ("python-rdflib" ,python-rdflib)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)
- ("python-requests" ,python-requests)
- ("python-ruamel.yaml" ,python-ruamel.yaml)
- ("python-setuptools" ,python-setuptools)
- ("python-typing-extensions" ,python-typing-extensions)))
- (native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-pytest-runner" ,python-pytest-runner)))
- (home-page "https://github.com/common-workflow-language/schema_salad")
- (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
- (description
- "Salad is a schema language for describing JSON or YAML structured linked
-data documents. Salad schema describes rules for preprocessing, structural
-validation, and hyperlink checking for documents described by a Salad schema.
-Salad supports rich data modeling with inheritance, template specialization,
-object identifiers, object references, documentation generation, code
-generation, and transformation to RDF. Salad provides a bridge between document
-and record oriented data modeling and the Semantic Web.")
- (license license:asl2.0)))
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 6e0c909..be531f6 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -61,7 +61,7 @@
("python-mock" ,python-mock)
("python-subprocess32" ,python-subprocess32)
("python-ruamel.yaml" ,python-ruamel.yaml)
- ("python-cachecontrol" ,python-cachecontrol)
+ ("python-cachecontrol" ,python-cachecontrol-0.11)
("python-lxml" ,python-lxml)
("python-mypy-extensions" ,python-mypy-extensions)
("python-mistune" ,python-mistune)
@@ -89,78 +89,3 @@
(description
"Common workflow language reference implementation")
(license license:asl2.0))))
-
-(define-public python-cachecontrol
- (package
- (name "python-cachecontrol")
- (version "0.11.7")
- (source
- (origin
- (method url-fetch)
- ;; Pypi does not have tests.
- (uri (string-append
- "https://github.com/ionrock/cachecontrol/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "1yfhwihx1b1xjsx0r19va2m0r2s91im03x4d7pwzp87368f2lkkp"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f)) ;; Recent version breaks on cherrypy
- (native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-redis" ,python-redis)
- ("python-webtest" ,python-webtest)
- ("python-mock" ,python-mock)))
- (propagated-inputs
- `(("python-requests" ,python-requests)
- ("python-lockfile" ,python-lockfile)))
- (home-page "https://github.com/ionrock/cachecontrol")
- (synopsis "The httplib2 caching algorithms for use with requests")
- (description "CacheControl is a port of the caching algorithms in
-@code{httplib2} for use with @code{requests} session objects.")
- (license license:asl2.0)))
-
-
-(define-public python-schema-salad
- (let ((commit "eb85c3d49b99b7643e8a12248e2dc05504910c1e"))
- (package
- (name "python-schema-salad")
- (version "3.0.20181129082112")
- (source
- (origin
- ; (method url-fetch)
- ; (uri (pypi-uri "schema-salad" version))
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/genenetwork/schema_salad.git") ;; my repo for Python3.7
- (commit commit)))
- (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
- (sha256
- (base32
- "174f224zzjr0nbjlq3ypciyfijnibasysrgjswvx8yhan2dizlhr"))))
- (build-system python-build-system)
- (arguments `(#:tests? #f)) ;; CWL includes no tests.
- (inputs
- `(("python-cython" ,python-cython)
- ("python-setuptools" ,python-setuptools)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)
- ("python-mistune" ,python-mistune)))
- (propagated-inputs
- `(("python-rdflib" ,python-rdflib)
- ("python-avro" ,python-avro)
- ("python-pyyaml" ,python-pyyaml)
- ("python-requests" ,python-requests)
- ("python-shellescape" ,python-shellescape)
- ))
- (home-page
- "https://github.com/common-workflow-language/common-workflow-language")
- (synopsis
- "Schema Annotations for Linked Avro Data (SALAD)")
- (description
- "Schema Annotations for Linked Avro Data (SALAD)")
- (license license:asl2.0))))
-
-; (define-public python2-schema-salad
-; (package-with-python2 python-schema-salad))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index c343815..46122ce 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1134,3 +1134,78 @@ spreadsheets without the need for COM objects.")
(sha256
(base32
"1lg1klrczvzfan89y3bl9ykrknl3nb01vvai37fkww24apzyibjf"))))))
+
+(define-public python-arvados-python-client
+ (package
+ (name "python-arvados-python-client")
+ (version "2.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "arvados-python-client" version))
+ (sha256
+ (base32
+ "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; tests not included?
+ (propagated-inputs
+ `(("python-ciso8601" ,python-ciso8601)
+ ("python-future" ,python-future)
+ ;("python-google-api-python-client" ,python-google-api-python-client)
+ ("python-google-api-client" ,python-google-api-client)
+ ("python-httplib2" ,python-httplib2)
+ ("python-pycurl" ,python-pycurl)
+ ("python-ruamel.yaml" ,python-ruamel.yaml-0.15)
+ ("python-setuptools" ,python-setuptools)
+ ("python-ws4py" ,python-ws4py)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-oauth2client" ,python-oauth2client)
+ ("python-pbr" ,python-pbr-1.6.0)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-uritemplate" ,python-uritemplate)))
+ (home-page "https://arvados.org")
+ (synopsis "Arvados client library")
+ (description "This package provides the arvados module, an API client for
+Arvados. It also includes higher-level functions to help you write Crunch
+scripts, and command-line tools to store and retrieve data in the Keep storage
+server.")
+ (license license:asl2.0)))
+
+(define-public python-schema-salad
+ (package
+ (name "python-schema-salad")
+ (version "5.0.20200416112825")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "schema-salad" version))
+ (sha256
+ (base32
+ "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-cachecontrol" ,python-cachecontrol-0.11)
+ ("python-lockfile" ,python-lockfile)
+ ("python-mistune" ,python-mistune)
+ ("python-rdflib" ,python-rdflib)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+ ("python-requests" ,python-requests)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-setuptools" ,python-setuptools)
+ ("python-typing-extensions" ,python-typing-extensions)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://github.com/common-workflow-language/schema_salad")
+ (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
+ (description
+ "Salad is a schema language for describing JSON or YAML structured linked
+data documents. Salad schema describes rules for preprocessing, structural
+validation, and hyperlink checking for documents described by a Salad schema.
+Salad supports rich data modeling with inheritance, template specialization,
+object identifiers, object references, documentation generation, code
+generation, and transformation to RDF. Salad provides a bridge between document
+and record oriented data modeling and the Semantic Web.")
+ (license license:asl2.0)))