Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Fri, 7 Mar 2025 18:51:02 UTC
Severity: normal
Tags: patch
Done: Steve George <steve <at> futurile.net>
Bug is archived. No further changes may be made.
Message #230 received at 76835 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 76835 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH v3 36/40] gnu: Add snakemake. Date: Mon, 10 Mar 2025 03:16:41 +0100
* gnu/packages/python-science.scm (snakemake): New variable.
---
gnu/packages/python-science.scm | 122 ++++++++++++++++++++++++++++++++
1 file changed, 122 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index ac16401254..7ccd991478 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -27,6 +27,7 @@
;;; Copyright © 2024 Marco Baggio <marco.baggio <at> mdc-berlin.de>
;;; Copyright © 2024 Nicolas Graves <ngraves <at> ngraves.fr>
;;; Copyright © 2024 Rick Huijzer <ikbenrickhuyzer <at> gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -67,6 +68,7 @@ (define-module (gnu packages python-science)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages pcre)
+ #:use-module (gnu packages package-management)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
@@ -82,6 +84,7 @@ (define-module (gnu packages python-science)
#:use-module (gnu packages ssh)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -4410,6 +4413,125 @@ (define-public python-libneuroml
neuronal models")
(license license:bsd-3)))
+(define-public snakemake
+ (package
+ (name "snakemake")
+ (version "8.29.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "snakemake" version))
+ (sha256
+ (base32 "1ilpmrjmnc529p4gw2x23ik1d8b5pm6k1dhq08dknvfjsf3vgyjr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ ;; XXX: Unclear why these tests fail.
+ "--ignore=tests/test_report_href/test_script.py"
+ "--ignore=tests/test_script_py/scripts/test_explicit_import.py"
+ "--ignore=tests/test_output_index.py"
+ ;; We don't care about testing old python <at> 3.7 on Guix.
+ "--ignore=tests/test_conda_python_3_7_script/test_script.py"
+ ;; Those require additional snakemake plugins.
+ "--ignore=tests/test_api.py"
+ "--ignore=tests/test_executor_test_suite.py"
+ ;; We don't care about lints.
+ "--ignore=tests/test_linting.py"
+ ;; These tests attempt to change S3 buckets on AWS and fail
+ ;; because there are no AWS credentials.
+ "--ignore=tests/test_tibanna"
+ ;; It's a similar story with this test, which requires access
+ ;; to the Google Storage service.
+ "--ignore=tests/test_google_lifesciences")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'avoid-assets-download
+ (lambda _
+ (substitute* "setup.py"
+ (("^from assets import Assets") "")
+ (("^Assets\\.deploy\\(\\)") ""))))
+ ;; 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 _
+ (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* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" "/tmp")))))))
+ (inputs
+ (list python-appdirs
+ python-conda-inject
+ python-configargparse
+ python-connection-pool
+ python-docutils
+ python-dpath
+ python-gitpython
+ python-humanfriendly
+ python-immutables
+ python-jinja2
+ python-jsonschema
+ python-nbformat
+ python-packaging
+ python-psutil
+ python-pulp
+ python-pyyaml
+ python-requests
+ python-reretry
+ python-smart-open
+ python-snakemake-interface-common
+ python-snakemake-interface-executor-plugins
+ python-snakemake-interface-report-plugins
+ python-snakemake-interface-storage-plugins
+ python-tabulate
+ python-throttler
+ python-wrapt
+ python-yte))
+ (native-inputs
+ (list python-numpy
+ python-pandas
+ python-setuptools
+ python-tomli
+ 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)))
+
;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above by existing packages with similar
--
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1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.