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-rw-r--r--gn/packages/bioinformatics.scm132
1 files changed, 131 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3e276af..09a706b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -34,9 +34,13 @@
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-science)
+ #:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
- #:use-module (gnu packages statistics))
+ #:use-module (gnu packages serialization)
+ #:use-module (gnu packages statistics)
+ #:use-module (gnu packages time))
(define-public contra
(package
@@ -1226,3 +1230,129 @@ runApp(launch.browser=0, port=4206)~%\n"
(description
"")
(license #f))))
+
+(define-public bh20-seq-resource
+ (let ((commit "ddabd9390d2b221786ef58a6d85200eecf82ca2f")
+ (revision "1"))
+ (package
+ (name "bh20-seq-resource")
+ (version (git-version "1.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/arvados/bh20-seq-resource")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "04j8b7rz1vqczm6dlyvf1gx58idjhy0swmjbz4bm5r4zgpkps6mb"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-arvados-python-client" ,python-arvados-python-client)
+ ("python-flask" ,python-flask)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-schema-salad" ,python-schema-salad)))
+ (native-inputs
+ `(("git" ,(@ (gnu packages version-control) git))
+ ("python-oauth2client" ,python-oauth2client)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)
+ ("python-uritemplate" ,python-uritemplate)))
+ (home-page "https://github.com/arvados/bh20-seq-resource")
+ (synopsis
+ "Tool to upload SARS-CoV-19 sequences and service to kick off analysis")
+ (description "This repository provides a sequence uploader for the
+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 "2.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "arvados-python-client" version))
+ (sha256
+ (base32
+ "1a363kdykj5jcrvh3q8wz06g6pqfnm2z48nfy64bls25pkiac1lr"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; tests not included?
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'loosen-version-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("ruamel.yaml.*") "ruamel.yaml',\n")
+ (("pbr<1.7.0") "pbr"))
+ #t)))))
+ (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)
+ ("python-setuptools" ,python-setuptools)
+ ("python-ws4py" ,python-ws4py)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-oauth2client" ,python-oauth2client)
+ ("python-pbr" ,python-pbr)
+ ("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 "5.0.20200302192450")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "schema-salad" version))
+ (sha256
+ (base32
+ "14vqmfnnvpdaqpajwzi9gyjxx4y2mbgi3y5x3kwk2zqjnnadciv3"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'loosen-version-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("CacheControl.*") "CacheControl',\n"))
+ #t)))))
+ (propagated-inputs
+ `(("python-cachecontrol" ,python-cachecontrol)
+ ("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)))