guix_mirror_bot pushed a commit to branch master
in repository guix.
commit ecd85c5f2e4090c58c9ec56dbe4850120d5faee7
Author: Nicolas Graves <[email protected]>
AuthorDate: Sun May 31 15:00:31 2026 +0200
gnu: Remove snakemake-7.
* gnu/packages/python-science.scm (snakemake-7): Delete variable.
Signed-off-by: Liliana Marie Prikler <[email protected]>
---
gnu/packages/python-science.scm | 93 -----------------------------------------
1 file changed, 93 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 16c963a3b0..d9cea3f086 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -6669,99 +6669,6 @@ 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-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-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-orsopy
(package
(name "python-orsopy")
