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gnu: Move all snakemake variants to python-science.
* gnu/packages/python-xyz.scm (snakemake-5, snakemake-6, snakemake-7): Move from here ... * gnu/packages/python-science.scm: ... to here. Change-Id: Ia771b316049f375183025e7617e6d0ddf06f99ff
This commit is contained in:
Sharlatan Hellseher
parent
127f232d1d
commit
74d1cf2583
2 changed files with 271 additions and 271 deletions
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@ -5004,6 +5004,277 @@ providing a clean and modern domain specific specification language (DSL) in
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Python style, together with a fast and comfortable execution environment.")
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Python style, together with a fast and comfortable execution environment.")
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(license license:expat)))
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(license license:expat)))
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(define-public snakemake-5
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(package
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(name "snakemake")
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(version "5.32.2")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/snakemake/snakemake")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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'(list
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;; We have no TES support.
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"--ignore=tests/test_tes.py"
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;; This test attempts to change S3 buckets on AWS and fails
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;; because there are no AWS credentials.
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"--ignore=tests/test_tibanna.py"
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;; It's a similar story with this test, which requires access
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;; to the Google Storage service.
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"--ignore=tests/test_google_lifesciences.py"
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;; Unclear failure.
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"-k" "not test_lint[long_run-positive]")
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'tabulate-compatibility
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(lambda _
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(substitute* "snakemake/dag.py"
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(("\"job\": rule,")
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"\"job\": rule.name,"))))
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(add-after 'unpack 'patch-version
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(lambda _
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(substitute* "setup.py"
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(("version=versioneer.get_version\\(\\)")
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(format #f "version=~s" #$version)))
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(substitute* '("snakemake/_version.py"
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"versioneer.py")
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(("0\\+unknown") #$version))))
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;; For cluster execution Snakemake will call Python. Since there is
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;; no suitable PYTHONPATH set, cluster execution will fail. We fix
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;; this by calling the snakemake wrapper instead.
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(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
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(lambda _
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(substitute* "snakemake/executors/__init__.py"
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(("\\{sys.executable\\} -m snakemake")
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(string-append #$output "/bin/snakemake")))))
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(add-before 'check 'pre-check
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(lambda _ (setenv "HOME" "/tmp"))))))
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(propagated-inputs
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(list python-appdirs
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python-configargparse
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python-datrie
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python-docutils
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python-gitpython
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python-jinja2
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python-jsonschema
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python-nbformat
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python-networkx
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python-psutil
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python-pulp
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python-pyyaml
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python-ratelimiter
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python-requests
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python-toposort
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python-wrapt))
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(native-inputs
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(list git-minimal
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python-wrapper
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python-pytest
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python-pandas
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python-requests-mock
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python-setuptools
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python-wheel))
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(home-page "https://snakemake.readthedocs.io")
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(synopsis "Python-based execution environment for make-like workflows")
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(description
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"Snakemake aims to reduce the complexity of creating workflows by
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providing a clean and modern domain specific specification language (DSL) in
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Python style, together with a fast and comfortable execution environment.")
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(license license:expat)))
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(define-public snakemake-6
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(package
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(inherit snakemake-5)
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(name "snakemake")
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(version "6.15.5")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/snakemake/snakemake")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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'(list
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;; This test attempts to change S3 buckets on AWS and fails
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;; because there are no AWS credentials.
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"--ignore=tests/test_tibanna.py"
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;; Unclear failure.
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"-k" "not test_lint[long_run-positive]")
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#:phases
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#~(modify-phases %standard-phases
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;; For cluster execution Snakemake will call Python. Since there is
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;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
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;; fix this by calling the snakemake wrapper instead.
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;; XXX: There is another instance of sys.executable on line 692, but
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;; it is not clear how to patch it.
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(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* "snakemake/executors/__init__.py"
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(("\\{sys.executable\\} -m snakemake")
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(string-append #$output "/bin/snakemake")))))
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(add-after 'unpack 'tabulate-compatibility
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(lambda _
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(substitute* "snakemake/dag.py"
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(("\"job\": rule,")
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"\"job\": rule.name,"))))
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(add-after 'unpack 'patch-version
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(lambda _
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(substitute* "setup.py"
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(("version=versioneer.get_version\\(\\)")
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(format #f "version=~s" #$version)))
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(substitute* '("snakemake/_version.py"
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"versioneer.py")
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(("0\\+unknown") #$version))))
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(add-before 'check 'pre-check
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(lambda _ (setenv "HOME" "/tmp"))))))
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(propagated-inputs
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(list python-appdirs
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python-configargparse
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python-connection-pool
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python-datrie
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python-docutils
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python-filelock
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python-gitpython
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python-jinja2
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python-jsonschema
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python-nbformat
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python-networkx
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python-psutil
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python-pulp
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python-pyyaml
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python-py-tes
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python-ratelimiter
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python-requests
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python-smart-open
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python-stopit
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python-tabulate
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python-toposort
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python-wrapt))
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(native-inputs
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(list git-minimal
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python-wrapper
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python-pytest
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python-pandas
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python-requests-mock
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python-setuptools
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python-wheel))))
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(define-public snakemake-7
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(package
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(inherit snakemake-6)
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(name "snakemake")
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(version "7.32.4")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/snakemake/snakemake")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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;; This test attempts to change S3 buckets on AWS and fails
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;; because there are no AWS credentials.
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'(list "--ignore=tests/test_tibanna.py"
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;; It's a similar story with this test, which requires access to
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;; the Google Storage service.
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"--ignore=tests/test_google_lifesciences.py"
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"--ignore-glob=tests/test_conda_python_3_7_script/*"
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;; We don't have a slurm installation in the build environment
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"--ignore=tests/test_slurm.py")
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#:phases
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#~(modify-phases %standard-phases
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;; For cluster execution Snakemake will call Python. Since there is
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;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
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;; fix this by calling the snakemake wrapper instead.
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(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* "snakemake/executors/__init__.py"
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(("self\\.get_python_executable\\(\\),")
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"")
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(("\"-m snakemake\"")
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(string-append "\"" #$output
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"/bin/snakemake" "\""))
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;; The snakemake command produced by format_job_exec contains
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;; references to /gnu/store. Prior to patching above that's
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;; just a reference to Python; after patching it's a reference
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;; to the snakemake executable.
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;;
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;; In Tibanna execution mode Snakemake arranges for a certain
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;; Docker image to be deployed to AWS. It then passes its own
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;; command line to Tibanna. This is misguided because it only
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;; ever works if the local Snakemake command was run inside
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;; the same Docker image. In the case of using Guix this is
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;; never correct, so we need to replace the store reference.
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(("tibanna_args.command = command")
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(string-append
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"tibanna_args.command = command.replace('"
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#$output "/bin/snakemake', 'python3 -m snakemake')")))))
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(add-after 'unpack 'patch-version
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(lambda _
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(substitute* "setup.py"
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(("version=versioneer.get_version\\(\\)")
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(format #f "version=~s" #$version)))
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(substitute* '("snakemake/_version.py"
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"versioneer.py")
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(("0\\+unknown") #$version))))
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(add-before 'check 'pre-check
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(lambda _ (setenv "HOME" "/tmp"))))))
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(propagated-inputs
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(list python-appdirs
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python-configargparse
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python-connection-pool
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python-datrie
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python-docutils
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python-filelock
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python-gitpython
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python-humanfriendly
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python-jinja2
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python-jsonschema
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python-nbformat
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python-networkx
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python-psutil
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python-pulp
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python-pyyaml
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python-py-tes
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python-requests
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python-retry
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python-reretry
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python-smart-open
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python-stopit
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python-tabulate
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python-throttler
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python-toposort
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python-wrapt
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python-yte))
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(native-inputs
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(list git-minimal
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python-wrapper
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python-pytest
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python-pandas
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python-requests-mock
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python-setuptools
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python-wheel))))
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;;;
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;;;
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;;; Avoid adding new packages to the end of this file. To reduce the chances
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;;; Avoid adding new packages to the end of this file. To reduce the chances
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;;; of a merge conflict, place them above by existing packages with similar
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;;; of a merge conflict, place them above by existing packages with similar
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@ -15155,277 +15155,6 @@ approach.")
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"This is a Python package for easy throttling with asyncio support.")
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"This is a Python package for easy throttling with asyncio support.")
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(license license:expat)))
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(license license:expat)))
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(define-public snakemake-5
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(package
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(name "snakemake")
|
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(version "5.32.2")
|
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(source
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(origin
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(method git-fetch)
|
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(uri (git-reference
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(url "https://github.com/snakemake/snakemake")
|
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(commit (string-append "v" version))))
|
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(file-name (git-file-name name version))
|
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(sha256
|
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||||||
(base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm"))))
|
|
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(build-system pyproject-build-system)
|
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(arguments
|
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||||||
(list
|
|
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#:test-flags
|
|
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'(list
|
|
||||||
;; We have no TES support.
|
|
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"--ignore=tests/test_tes.py"
|
|
||||||
;; This test attempts to change S3 buckets on AWS and fails
|
|
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;; because there are no AWS credentials.
|
|
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"--ignore=tests/test_tibanna.py"
|
|
||||||
;; It's a similar story with this test, which requires access
|
|
||||||
;; to the Google Storage service.
|
|
||||||
"--ignore=tests/test_google_lifesciences.py"
|
|
||||||
;; Unclear failure.
|
|
||||||
"-k" "not test_lint[long_run-positive]")
|
|
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#:phases
|
|
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#~(modify-phases %standard-phases
|
|
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(add-after 'unpack 'tabulate-compatibility
|
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(lambda _
|
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(substitute* "snakemake/dag.py"
|
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(("\"job\": rule,")
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"\"job\": rule.name,"))))
|
|
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(add-after 'unpack 'patch-version
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|
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(lambda _
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(substitute* "setup.py"
|
|
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(("version=versioneer.get_version\\(\\)")
|
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(format #f "version=~s" #$version)))
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(substitute* '("snakemake/_version.py"
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"versioneer.py")
|
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(("0\\+unknown") #$version))))
|
|
||||||
;; For cluster execution Snakemake will call Python. Since there is
|
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;; no suitable PYTHONPATH set, cluster execution will fail. We fix
|
|
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;; this by calling the snakemake wrapper instead.
|
|
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(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
|
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(lambda _
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(substitute* "snakemake/executors/__init__.py"
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(("\\{sys.executable\\} -m snakemake")
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(string-append #$output "/bin/snakemake")))))
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(add-before 'check 'pre-check
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(lambda _ (setenv "HOME" "/tmp"))))))
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|
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(propagated-inputs
|
|
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(list python-appdirs
|
|
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python-configargparse
|
|
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python-datrie
|
|
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python-docutils
|
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python-gitpython
|
|
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python-jinja2
|
|
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python-jsonschema
|
|
||||||
python-nbformat
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|
||||||
python-networkx
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python-psutil
|
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python-pulp
|
|
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python-pyyaml
|
|
||||||
python-ratelimiter
|
|
||||||
python-requests
|
|
||||||
python-toposort
|
|
||||||
python-wrapt))
|
|
||||||
(native-inputs
|
|
||||||
(list git-minimal
|
|
||||||
python-wrapper
|
|
||||||
python-pytest
|
|
||||||
python-pandas
|
|
||||||
python-requests-mock
|
|
||||||
python-setuptools
|
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||||||
python-wheel))
|
|
||||||
(home-page "https://snakemake.readthedocs.io")
|
|
||||||
(synopsis "Python-based execution environment for make-like workflows")
|
|
||||||
(description
|
|
||||||
"Snakemake aims to reduce the complexity of creating workflows by
|
|
||||||
providing a clean and modern domain specific specification language (DSL) in
|
|
||||||
Python style, together with a fast and comfortable execution environment.")
|
|
||||||
(license license:expat)))
|
|
||||||
|
|
||||||
(define-public snakemake-6
|
|
||||||
(package
|
|
||||||
(inherit snakemake-5)
|
|
||||||
(name "snakemake")
|
|
||||||
(version "6.15.5")
|
|
||||||
(source
|
|
||||||
(origin
|
|
||||||
(method git-fetch)
|
|
||||||
(uri (git-reference
|
|
||||||
(url "https://github.com/snakemake/snakemake")
|
|
||||||
(commit (string-append "v" version))))
|
|
||||||
(file-name (git-file-name name version))
|
|
||||||
(sha256
|
|
||||||
(base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
|
|
||||||
(build-system pyproject-build-system)
|
|
||||||
(arguments
|
|
||||||
(list
|
|
||||||
#:test-flags
|
|
||||||
'(list
|
|
||||||
;; This test attempts to change S3 buckets on AWS and fails
|
|
||||||
;; because there are no AWS credentials.
|
|
||||||
"--ignore=tests/test_tibanna.py"
|
|
||||||
;; Unclear failure.
|
|
||||||
"-k" "not test_lint[long_run-positive]")
|
|
||||||
#:phases
|
|
||||||
#~(modify-phases %standard-phases
|
|
||||||
;; For cluster execution Snakemake will call Python. Since there is
|
|
||||||
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
|
|
||||||
;; fix this by calling the snakemake wrapper instead.
|
|
||||||
|
|
||||||
;; XXX: There is another instance of sys.executable on line 692, but
|
|
||||||
;; it is not clear how to patch it.
|
|
||||||
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
|
|
||||||
(lambda* (#:key outputs #:allow-other-keys)
|
|
||||||
(substitute* "snakemake/executors/__init__.py"
|
|
||||||
(("\\{sys.executable\\} -m snakemake")
|
|
||||||
(string-append #$output "/bin/snakemake")))))
|
|
||||||
(add-after 'unpack 'tabulate-compatibility
|
|
||||||
(lambda _
|
|
||||||
(substitute* "snakemake/dag.py"
|
|
||||||
(("\"job\": rule,")
|
|
||||||
"\"job\": rule.name,"))))
|
|
||||||
(add-after 'unpack 'patch-version
|
|
||||||
(lambda _
|
|
||||||
(substitute* "setup.py"
|
|
||||||
(("version=versioneer.get_version\\(\\)")
|
|
||||||
(format #f "version=~s" #$version)))
|
|
||||||
(substitute* '("snakemake/_version.py"
|
|
||||||
"versioneer.py")
|
|
||||||
(("0\\+unknown") #$version))))
|
|
||||||
(add-before 'check 'pre-check
|
|
||||||
(lambda _ (setenv "HOME" "/tmp"))))))
|
|
||||||
(propagated-inputs
|
|
||||||
(list python-appdirs
|
|
||||||
python-configargparse
|
|
||||||
python-connection-pool
|
|
||||||
python-datrie
|
|
||||||
python-docutils
|
|
||||||
python-filelock
|
|
||||||
python-gitpython
|
|
||||||
python-jinja2
|
|
||||||
python-jsonschema
|
|
||||||
python-nbformat
|
|
||||||
python-networkx
|
|
||||||
python-psutil
|
|
||||||
python-pulp
|
|
||||||
python-pyyaml
|
|
||||||
python-py-tes
|
|
||||||
python-ratelimiter
|
|
||||||
python-requests
|
|
||||||
python-smart-open
|
|
||||||
python-stopit
|
|
||||||
python-tabulate
|
|
||||||
python-toposort
|
|
||||||
python-wrapt))
|
|
||||||
(native-inputs
|
|
||||||
(list git-minimal
|
|
||||||
python-wrapper
|
|
||||||
python-pytest
|
|
||||||
python-pandas
|
|
||||||
python-requests-mock
|
|
||||||
python-setuptools
|
|
||||||
python-wheel))))
|
|
||||||
|
|
||||||
(define-public snakemake-7
|
|
||||||
(package
|
|
||||||
(inherit snakemake-6)
|
|
||||||
(name "snakemake")
|
|
||||||
(version "7.32.4")
|
|
||||||
(source
|
|
||||||
(origin
|
|
||||||
(method git-fetch)
|
|
||||||
(uri (git-reference
|
|
||||||
(url "https://github.com/snakemake/snakemake")
|
|
||||||
(commit (string-append "v" version))))
|
|
||||||
(file-name (git-file-name name version))
|
|
||||||
(sha256
|
|
||||||
(base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d"))))
|
|
||||||
(build-system pyproject-build-system)
|
|
||||||
(arguments
|
|
||||||
(list
|
|
||||||
#:test-flags
|
|
||||||
;; This test attempts to change S3 buckets on AWS and fails
|
|
||||||
;; because there are no AWS credentials.
|
|
||||||
'(list "--ignore=tests/test_tibanna.py"
|
|
||||||
;; It's a similar story with this test, which requires access to
|
|
||||||
;; the Google Storage service.
|
|
||||||
"--ignore=tests/test_google_lifesciences.py"
|
|
||||||
"--ignore-glob=tests/test_conda_python_3_7_script/*"
|
|
||||||
;; We don't have a slurm installation in the build environment
|
|
||||||
"--ignore=tests/test_slurm.py")
|
|
||||||
#:phases
|
|
||||||
#~(modify-phases %standard-phases
|
|
||||||
;; For cluster execution Snakemake will call Python. Since there is
|
|
||||||
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
|
|
||||||
;; fix this by calling the snakemake wrapper instead.
|
|
||||||
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
|
|
||||||
(lambda* (#:key outputs #:allow-other-keys)
|
|
||||||
(substitute* "snakemake/executors/__init__.py"
|
|
||||||
(("self\\.get_python_executable\\(\\),")
|
|
||||||
"")
|
|
||||||
(("\"-m snakemake\"")
|
|
||||||
(string-append "\"" #$output
|
|
||||||
"/bin/snakemake" "\""))
|
|
||||||
;; The snakemake command produced by format_job_exec contains
|
|
||||||
;; references to /gnu/store. Prior to patching above that's
|
|
||||||
;; just a reference to Python; after patching it's a reference
|
|
||||||
;; to the snakemake executable.
|
|
||||||
;;
|
|
||||||
;; In Tibanna execution mode Snakemake arranges for a certain
|
|
||||||
;; Docker image to be deployed to AWS. It then passes its own
|
|
||||||
;; command line to Tibanna. This is misguided because it only
|
|
||||||
;; ever works if the local Snakemake command was run inside
|
|
||||||
;; the same Docker image. In the case of using Guix this is
|
|
||||||
;; never correct, so we need to replace the store reference.
|
|
||||||
(("tibanna_args.command = command")
|
|
||||||
(string-append
|
|
||||||
"tibanna_args.command = command.replace('"
|
|
||||||
#$output "/bin/snakemake', 'python3 -m snakemake')")))))
|
|
||||||
(add-after 'unpack 'patch-version
|
|
||||||
(lambda _
|
|
||||||
(substitute* "setup.py"
|
|
||||||
(("version=versioneer.get_version\\(\\)")
|
|
||||||
(format #f "version=~s" #$version)))
|
|
||||||
(substitute* '("snakemake/_version.py"
|
|
||||||
"versioneer.py")
|
|
||||||
(("0\\+unknown") #$version))))
|
|
||||||
(add-before 'check 'pre-check
|
|
||||||
(lambda _ (setenv "HOME" "/tmp"))))))
|
|
||||||
(propagated-inputs
|
|
||||||
(list python-appdirs
|
|
||||||
python-configargparse
|
|
||||||
python-connection-pool
|
|
||||||
python-datrie
|
|
||||||
python-docutils
|
|
||||||
python-filelock
|
|
||||||
python-gitpython
|
|
||||||
python-humanfriendly
|
|
||||||
python-jinja2
|
|
||||||
python-jsonschema
|
|
||||||
python-nbformat
|
|
||||||
python-networkx
|
|
||||||
python-psutil
|
|
||||||
python-pulp
|
|
||||||
python-pyyaml
|
|
||||||
python-py-tes
|
|
||||||
python-requests
|
|
||||||
python-retry
|
|
||||||
python-reretry
|
|
||||||
python-smart-open
|
|
||||||
python-stopit
|
|
||||||
python-tabulate
|
|
||||||
python-throttler
|
|
||||||
python-toposort
|
|
||||||
python-wrapt
|
|
||||||
python-yte))
|
|
||||||
(native-inputs
|
|
||||||
(list git-minimal
|
|
||||||
python-wrapper
|
|
||||||
python-pytest
|
|
||||||
python-pandas
|
|
||||||
python-requests-mock
|
|
||||||
python-setuptools
|
|
||||||
python-wheel))))
|
|
||||||
|
|
||||||
(define-public python-pyqrcode
|
(define-public python-pyqrcode
|
||||||
(package
|
(package
|
||||||
(name "python-pyqrcode")
|
(name "python-pyqrcode")
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue