diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 132 |
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))) |