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authorEfraim Flashner2020-11-23 15:41:39 +0200
committerEfraim Flashner2020-11-23 15:41:39 +0200
commit4034fd9b19e6807d355c86726b33f6dc10a39664 (patch)
tree26ab62f567df2a27717139a46d4c69f846e01c26
parent8a66ab55cab786acb9cba38b387bbbc58fa35dfa (diff)
downloadguix-bioinformatics-4034fd9b19e6807d355c86726b33f6dc10a39664.tar.gz
upstream cwltools and dependant packages
-rw-r--r--gn/packages/bioinformatics.scm3
-rw-r--r--gn/packages/cwl.scm115
-rw-r--r--gn/packages/python.scm191
3 files changed, 1 insertions, 308 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 9784aca..25aece9 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -17,7 +17,6 @@
#:use-module (gn packages python)
#:use-module (gn packages twint)
#:use-module (gnu packages algebra)
- #:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bioconductor)
@@ -32,7 +31,6 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
- #:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages jemalloc)
@@ -51,7 +49,6 @@
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
- #:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
#:use-module (gnu packages web))
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
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index a9c2770..c8892be 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1,31 +1,16 @@
(define-module (gn packages python)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
- #:use-module (gnu packages attr)
- #:use-module (gnu packages base)
- #:use-module (gnu packages bioinformatics)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
- #:use-module (gnu packages databases)
#:use-module (gnu packages fontutils)
- #:use-module (gnu packages gcc)
#:use-module (gnu packages ghostscript)
- #:use-module (gnu packages glib)
- #:use-module (gnu packages gnupg)
#:use-module (gnu packages graphviz)
- #:use-module (gnu packages gtk)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
- #:use-module (gnu packages imagemagick)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
- #:use-module (gnu packages maths)
- #:use-module (gnu packages multiprecision)
- #:use-module (gnu packages networking)
- #:use-module (gnu packages ncurses)
#:use-module (gnu packages pcre)
- #:use-module (gnu packages perl)
- #:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-crypto)
@@ -37,20 +22,12 @@
#:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tcl)
- #:use-module (gnu packages tex)
- #:use-module (gnu packages texinfo)
#:use-module (gnu packages time)
- #:use-module (gnu packages tls)
- #:use-module (gnu packages web)
- #:use-module (gnu packages xml)
- #:use-module (gnu packages xorg)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
- #:use-module (guix build-system gnu)
#:use-module (guix build-system python)
- #:use-module (guix build-system trivial)
#:use-module (srfi srfi-1))
(define-public python-pyvcf
@@ -172,56 +149,6 @@ functions.")
(define-public python2-plotly-3.2.1
(package-with-python2 python-plotly-3.2.1))
-(define-public python-bagit; guix candidate
- (package
- (name "python-bagit")
- (version "1.7.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "bagit" version))
- (sha256
- (base32
- "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
- (build-system python-build-system)
- (inputs
- `(("python-setuptools-scm" ,python-setuptools-scm)
- ("python-coverage" ,python-coverage)
- ("python-mock" ,python-mock)))
- (arguments `(#:tests? #f)) ;; No tests.
- (home-page "https://pypi.python.org/pypi/bagit")
- (synopsis "Create and validate BagIt packages")
- (description
- "Create and validate BagIt packages")
- (license license:gpl2)))
-
-(define-public python-prov ; guix candidate
-(package
- (name "python-prov")
- (version "1.5.3")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "prov" version))
- (sha256
- (base32
- "1a9h406laclxalmdny37m0yyw7y17n359akclbahimdggq853jd0"))))
- (build-system python-build-system)
- (inputs
- `(("python-rdflib" ,python-rdflib)
- ("python-lxml" ,python-lxml)
- ("python-networkx" ,python-networkx)
- ("python-dateutil" ,python-dateutil)
- ("python-pydot" ,python-pydot)
- ("graphviz" ,graphviz) ; for testing
- ))
- (home-page "https://github.com/trungdong/prov")
- (synopsis
- "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)")
- (description
- "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)")
- (license license:expat)))
-
(define-public python-subprocess32 ; guix candidate
(package
(name "python-subprocess32")
@@ -398,30 +325,6 @@ Python 3 support.")
(define-public python2-avro
(package-with-python2 python-avro))
-(define-public python-shellescape ; guix ready
- (package
- (name "python-shellescape")
- (version "3.4.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "shellescape" version))
- (sha256
- (base32
- "0n5ky1b2vw2y0d4xl3qybyp2rk0gq5frjs8nr8ak6mgj2fyb4676"))))
- (build-system python-build-system)
- (native-inputs
- `(("python-setuptools" ,python-setuptools)))
- (home-page "https://github.com/chrissimpkins/shellescape")
- (synopsis
- "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)")
- (description
- "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)")
- (license license:expat)))
-
-(define-public python2-shellescape
- (package-with-python2 python-shellescape))
-
; env IPFS_PATH=/export/ipfs/ ipfs add -r htmlgen/
; added QmUD9LMJTE8q5wYkUyAwLdz2QCGXWt457iFnyYQAGfsN3j htmlgen/htmlgen-2.2.2-gn.tar.gz
@@ -829,49 +732,6 @@ the older versions.")
(license license:expat)
)))
-(define-public python-mypy-extensions
-(package
- (name "python-mypy-extensions")
- (version "0.4.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "mypy_extensions" version))
- (sha256
- (base32
- "04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p"))))
- (build-system python-build-system)
- (inputs
- `(("python-version" ,python-version)))
- (home-page "http://www.mypy-lang.org/")
- (synopsis
- "Experimental type system extensions for programs checked with the mypy typechecker.")
- (description
- "Experimental type system extensions for programs checked with the mypy typechecker.")
- (license #f))
-)
-
-
-(define-public python-arcp
-(package
- (name "python-arcp")
- (version "0.2.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "arcp" version))
- (sha256
- (base32
- "0h8sn0mlb6vb8wqqnqc4pxdklrkyx3p72afdhm7b9kyalrqzd7dd"))))
- (build-system python-build-system)
- (home-page "http://arcp.readthedocs.io/")
- (synopsis
- "arcp (Archive and Package) URI parser and generator")
- (description
- "arcp (Archive and Package) URI parser and generator")
- (license license:asl2.0))
-)
-
(define-public python2-pp
(package
(name "python2-pp")
@@ -1032,19 +892,6 @@ spreadsheets without the need for COM objects.")
(define-public python2-admiral
(package-with-python2 python-admiral))
-(define-public python-cachecontrol-0.11
- (package
- (inherit python-cachecontrol)
- (name "python-cachecontrol")
- (version "0.11.7")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "CacheControl" version))
- (sha256
- (base32
- "07jsfhlbcwgqg6ayz8nznzaqg5rmxqblbzxz1qvg5wc44pcjjy4g"))))))
-
(define-public python-pbr-1.6.0
(package
(inherit python-pbr)
@@ -1097,44 +944,6 @@ 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 "7.0.20200811075006")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "schema-salad" version))
- (sha256
- (base32
- "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg"))))
- (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)
- ;; This needs to be fixed before upstreaming - fixed?
- ("python-ruamel.yaml" ,python-ruamel.yaml)
- ("python-setuptools" ,python-setuptools)
- ("python-typing-extensions" ,python-typing-extensions)))
- (native-inputs
- `(("python-pytest" ,python-pytest-4)
- ("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)))
-
(define-public python-pyshex
(package
(name "python-pyshex")