guix_mirror_bot pushed a commit to branch master
in repository guix.
commit a168a67d20f402f88a81de74a7ee6e3d11f324fe
Author: Nicolas Graves <[email protected]>
AuthorDate: Sun May 31 15:00:47 2026 +0200
gnu: Remove snakemake-6.
* gnu/packages/python-science.scm (snakemake-6): Delete variable.
Signed-off-by: Liliana Marie Prikler <[email protected]>
---
gnu/packages/python-science.scm | 85 -----------------------------------------
1 file changed, 85 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d9cea3f086..700127f2dc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -6584,91 +6584,6 @@ 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
- (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"))
- (snippet #~(delete-file "versioneer.py"))))
- (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"
- ;; E ModuleNotFoundError: No module named 'google'
- "--ignore=tests/test_google_lifesciences.py"
- ;; Unclear failures.
- "-k" "not test_lint")
- #: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-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-versioneer))
- (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 python-orsopy
(package
(name "python-orsopy")
