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authorRicardo Wurmus <rekado@elephly.net>2022-05-20 13:59:38 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-05-20 14:18:12 +0200
commit5fd82d7bbd30e17fa1e542037dd48e34a0a1c776 (patch)
tree9ecf7f2f190bd4e30cf7cb754b88fd2be0f460bd
parent192c7229284b9499257b6b4ac46a17b93ffd0c52 (diff)
gnu: Add snakemake-6.
* gnu/packages/python-xyz.scm (snakemake-6): New variable.
-rw-r--r--gnu/packages/python-xyz.scm68
1 files changed, 68 insertions, 0 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index cdb6300117..96a739f90e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10194,6 +10194,74 @@ 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)
+ (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 python-build-system)
+ (arguments
+ '(#: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 (assoc-ref outputs "out")
+ "/bin/snakemake")))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" "/tmp")
+ ;; This test attempts to change S3 buckets on AWS and fails
+ ;; because there are no AWS credentials.
+ (delete-file "tests/test_tibanna.py")
+ (invoke "pytest")))))))
+ (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))))
+
(define-public python-pyqrcode
(package
(name "python-pyqrcode")