From: Arun Isaac <arunisaac@systemreboot.net>
To: 69736@debbugs.gnu.org
Cc: Arun Isaac <arunisaac@systemreboot.net>,
Arun Isaac <arunisaac@systemreboot.net>
Subject: [bug#69736] [PATCH 7/7] gnu: Add python-toil.
Date: Mon, 11 Mar 2024 18:22:42 +0000 [thread overview]
Message-ID: <79a9044f3ced28df0b987c383f25b7fb657aac6e.1710180345.git.arunisaac@systemreboot.net> (raw)
In-Reply-To: <cover.1710180345.git.arunisaac@systemreboot.net>
* gnu/packages/bioinformatics.scm (python-toil): New variable.
Change-Id: I1a6c071eaa9169c1e0cd7c74d1117490ee7bf267
---
gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++
1 file changed, 62 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 68577ded17..aed57796cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -87,6 +87,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages dlang)
+ #:use-module (gnu packages docker)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
@@ -5338,6 +5339,67 @@ (define-public python-cwltool
(modify-inputs (package-inputs cwltool)
(delete "node")))))
+(define-public python-toil
+ (package
+ (name "python-toil")
+ (version "6.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "toil" version))
+ (sha256
+ (base32
+ "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'disable-optional-features
+ (lambda _
+ (substitute* "requirements-cwl.txt"
+ ;; Loosen version restrictions on ruamel.yaml.
+ (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n")
+ ;; Remove optional dependency on galaxy-util and
+ ;; galaxy-tool-util. TODO: Package these and restore these
+ ;; dependencies.
+ (("galaxy-util[^\n]*") "")
+ (("galaxy-tool-util[^\n]*") ""))
+ ;; Disable optional wdl, wes and mesos features. We don't yet
+ ;; have dependencies packaged for them. TODO: Package these
+ ;; dependencies and enable these features.
+ (substitute* "setup.py"
+ (("\"wdl\",") "")
+ (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]")
+ "toil-cwl-runner = toil.cwl.cwltoil:main")
+ (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "")
+ (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "")
+ (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") "")))))))
+ (propagated-inputs
+ (list python-addict
+ python-cachecontrol
+ python-configargparse
+ python-cwltool
+ python-dateutil
+ python-dill
+ python-docker
+ python-enlighten
+ python-psutil
+ python-pypubsub
+ python-pytz
+ python-pyyaml
+ python-requests
+ python-ruamel.yaml
+ python-typing-extensions-4.10
+ python-urllib3))
+ (home-page "https://github.com/DataBiosphere/toil")
+ (synopsis "Scalable, efficient and cross-platform workflow engine")
+ (description "Toil is a scalable, efficient, cross-platform pipeline
+management system, written entirely in Python, and designed around the
+principles of functional programming.")
+ (license (list license:asl2.0 ;; main license
+ license:expat)))) ;; src/toil/batchSystems/lsf.py and
+ ;; src/toil/batchSystems/lsfHelper.py
+
(define-public python-dendropy
(package
(name "python-dendropy")
--
2.41.0
next prev parent reply other threads:[~2024-03-11 18:28 UTC|newest]
Thread overview: 16+ messages / expand[flat|nested] mbox.gz Atom feed top
2024-03-11 18:11 [bug#69736] [PATCH 0/7] Add toil Arun Isaac
2024-03-11 18:22 ` [bug#69736] [PATCH 1/7] gnu: Add python-typing-extensions-4.10 Arun Isaac
2024-03-11 18:22 ` [bug#69736] [PATCH 2/7] gnu: Add python-pypubsub Arun Isaac
2024-03-11 18:22 ` [bug#69736] [PATCH 3/7] gnu: Add python-addict Arun Isaac
2024-03-11 18:22 ` [bug#69736] [PATCH 4/7] gnu: Add python-prefixed Arun Isaac
2024-03-11 18:22 ` [bug#69736] [PATCH 5/7] gnu: Add python-enlighten Arun Isaac
2024-03-11 18:22 ` [bug#69736] [PATCH 6/7] gnu: Add python-cwltool Arun Isaac
2024-03-11 18:22 ` Arun Isaac [this message]
2024-07-01 2:54 ` [bug#69736] [PATCH 0/7] Add toil jgart via Guix-patches via
2024-07-03 15:05 ` Arun Isaac
2024-07-03 15:07 ` [bug#69736] [PATCH v2 1/6] gnu: Add python-pypubsub Arun Isaac
2024-07-03 15:07 ` [bug#69736] [PATCH v2 2/6] gnu: Add python-addict Arun Isaac
2024-07-03 15:07 ` [bug#69736] [PATCH v2 3/6] gnu: Add python-prefixed Arun Isaac
2024-07-03 15:07 ` [bug#69736] [PATCH v2 4/6] gnu: Add python-enlighten Arun Isaac
2024-07-03 15:07 ` [bug#69736] [PATCH v2 5/6] gnu: Add python-cwltool Arun Isaac
2024-07-03 15:07 ` [bug#69736] [PATCH v2 6/6] gnu: Add python-toil Arun Isaac
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