From f2f3d03d007fb906120c7f3cfaba5b925802715a Mon Sep 17 00:00:00 2001 From: Marco De La Pierre Date: Fri, 20 Jan 2023 20:05:26 +0800 Subject: Add nf-core-tools, and three remainder deps (#34466) * nextflow recipe: added latest stable version * tower-cli recipe: added latest release * recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli * recipes nf-tower-agent and nf-tower-cli: small fix * nf-core-tools recipe: added most py- dependencies * nf-core-tools: recipe without galaxy-tool-util (for testing) * fixed typos in py-yacman recipe * fixed typos in py-pytest-workflow recipe * fixed typo in nf-core-tools recipe * fixed typos in py-yacman recipe * fixes in recipes for py-questionary and py-url-normalize * fixes to py-yacman recipe * style fixes to py- packages that are dependencies to nf-core-tools * fix in py-requests-cache recipe * added missing dep in py-requests-cache recipe * nf-core-tools deps: removed redundant python dep for py packages oyaml and piper * nf-core-tools recipe: final, incl dep on py-galaxy-tool-util * nf-core-tools: new version with extra dependency * added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps * nextflow and nf-core-tools packages: added my self as maintainer * style fixes * style fix for nf-core-tools recipe * added license to py-logmuse recipe * audit fixes * style fix after audit fix * py-galaxy-tool-util: added deps 1st bunch * audit/style fixes, including adding missing dep package * more audit/style fixes * more more audit/style fixes * moooore audit fixes * py-galaxy-tool-util: dependencies 2nd chunk * silly audit fix * py-galaxy-util deps: 3rd bunch - first 20 done * fixes * style fix * py-galaxy-tool-util: 4th bunch of deps * stashing dep recipe backbones for py-galaxy-tool-util * nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util * nf-core-tools: adding also py-galaxy-util, as wheel * fix * nextflow: added latest bugfix version * Update var/spack/repos/builtin/packages/nf-core-tools/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/nf-core-tools/package.py Co-authored-by: Adam J. Stewart * nf-core-tools pr: 1st bunch of review edits * nf-core-tools: 2nd bunch of review edits * adding back tower-agent and tower-cli as deprecated * nf-core-tools: 3rd bunch of review edits * small style fix * prepping py-galaxy-tool-util for further work * nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar * audit fixes * updates to py-galaxy-tool-util and its deps, still 2 to work on * one style fix * updated recipe for py-galaxy-util * updated recipe for py-pulsar-galaxy-lib * typo fix * shasum fixes * updated py-sqlalchemy from develop * added newest versions (today) for nf-tower-agent and nf-tower-cli * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart * adding 2nd bunch of nf-core deps from update/nextflow-tools * adding 3rd bunch of nf-core deps from update/nextflow-tools * 4th chunk of nf-core deps from update/nextflow-tools * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-pastedeploy/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-pebble/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-fastapi/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-fastapi/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-gunicorn/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-parsley/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-paste/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-paste/package.py Co-authored-by: Adam J. Stewart * py-gxformat2: added comment * py-lagom: now using github tarballs * fix for py-lagom * adding missing deps to py-fastapi-utils * another fix to py-lagom * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-lagom/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-supervisor/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-social-auth-core/package.py Co-authored-by: Adam J. Stewart * fixes from PR review * adding missing deps, from PR review * py-galaxy2cwl from github tarball, as per PR review * fix to py-tuswsgi, as per PR review * nf-tools: edits from PR review * adding 3x more galaxy deps * fix * fixing circular dep of py-poetry-plugin-export with py-poetry * added newest nf-core-tools version * Update var/spack/repos/builtin/packages/py-galaxy-util/package.py Co-authored-by: Adam J. Stewart * fix in py-poetry-plugin-export Co-authored-by: Adam J. Stewart --- .../builtin/packages/nf-core-tools/package.py | 46 ++++++++++++++++++++++ .../packages/py-galaxy-containers/package.py | 23 +++++++++++ .../packages/py-galaxy-job-metrics/package.py | 20 ++++++++++ .../packages/py-galaxy-objectstore/package.py | 21 ++++++++++ .../packages/py-galaxy-tool-util/package.py | 26 ++++++++++++ .../builtin/packages/py-galaxy-util/package.py | 32 +++++++++++++++ .../packages/py-poetry-plugin-export/package.py | 3 +- .../packages/py-pulsar-galaxy-lib/package.py | 29 ++++++++++++++ 8 files changed, 199 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/nf-core-tools/package.py create mode 100644 var/spack/repos/builtin/packages/py-galaxy-containers/package.py create mode 100644 var/spack/repos/builtin/packages/py-galaxy-job-metrics/package.py create mode 100644 var/spack/repos/builtin/packages/py-galaxy-objectstore/package.py create mode 100644 var/spack/repos/builtin/packages/py-galaxy-tool-util/package.py create mode 100644 var/spack/repos/builtin/packages/py-galaxy-util/package.py create mode 100644 var/spack/repos/builtin/packages/py-pulsar-galaxy-lib/package.py diff --git a/var/spack/repos/builtin/packages/nf-core-tools/package.py b/var/spack/repos/builtin/packages/nf-core-tools/package.py new file mode 100644 index 0000000000..11c2ed81e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/nf-core-tools/package.py @@ -0,0 +1,46 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class NfCoreTools(PythonPackage): + """A python package with helper tools for the nf-core community.""" + + homepage = "https://nf-co.re/tools" + pypi = "nf-core/nf-core-2.7.1.tar.gz" + maintainers = ["marcodelapierre"] + + version("2.7.2", sha256="585be3908b9b93ee9263b99dd779818d48d51f6e7f44a42aa79e626617e7af48") + version("2.7.1", sha256="90de62390314ef3141cee700667f017aa65c0346e40704a0f70d0662abcfb0db") + version("2.6", sha256="47d4df906a60006249284bbf0bb84cdec48303a699c7c0d0a26f404a50e0811a") + version("2.5.1", sha256="0303f6e3810ba1bc6ac843566ee9dea6b5edbf3527437dec5854b8c437456a4f") + + depends_on("nextflow@21.10.3:", type="run") + + depends_on("python@3.7:3", type=("build", "run")) + depends_on("py-setuptools@40.6:", type="build") + + depends_on("py-click", type=("build", "run")) + depends_on("py-filetype", type=("build", "run")) + depends_on("py-galaxy-tool-util", type=("build", "run")) + depends_on("py-gitpython", type=("build", "run")) + depends_on("py-jinja2", type=("build", "run")) + depends_on("py-jsonschema@3.0:", type=("build", "run")) + depends_on("py-markdown@3.3:", type=("build", "run")) + depends_on("py-packaging", type=("build", "run")) + depends_on("py-pre-commit", type=("build", "run")) + depends_on("py-prompt-toolkit@3.0.3:", type=("build", "run")) + depends_on("py-pytest@7.0.0:", type=("build", "run")) + depends_on("py-pytest-workflow@1.6.0:", type=("build", "run")) + depends_on("py-pyyaml", type=("build", "run")) + depends_on("py-questionary@1.8.0:", type=("build", "run")) + depends_on("py-refgenie", type=("build", "run")) + depends_on("py-requests", type=("build", "run")) + depends_on("py-requests-cache", type=("build", "run")) + depends_on("py-rich-click@1.0.0:", type=("build", "run")) + depends_on("py-rich@10.7.0:", type=("build", "run")) + depends_on("py-tabulate", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-galaxy-containers/package.py b/var/spack/repos/builtin/packages/py-galaxy-containers/package.py new file mode 100644 index 0000000000..537ae37634 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-galaxy-containers/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class PyGalaxyContainers(PythonPackage): + """The Galaxy containers module - interfaces for modeling and interacting + with container backends (docker and docker swarm currently). + """ + + homepage = "https://github.com/galaxyproject/galaxy" + pypi = "galaxy-containers/galaxy-containers-22.1.1.tar.gz" + + version("22.1.1", sha256="41e0003b18e580175d443cf21e9c2d2eb21a265c012164f7255cdb0c03a76334") + + depends_on("py-setuptools", type="build") + + depends_on("py-galaxy-util", type=("build", "run")) + depends_on("py-requests", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-galaxy-job-metrics/package.py b/var/spack/repos/builtin/packages/py-galaxy-job-metrics/package.py new file mode 100644 index 0000000000..d8679f33c7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-galaxy-job-metrics/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class PyGalaxyJobMetrics(PythonPackage): + """The Galaxy job metrics framework and default plugins.""" + + homepage = "https://github.com/galaxyproject/galaxy" + pypi = "galaxy-job-metrics/galaxy-job-metrics-22.1.1.tar.gz" + + version("22.1.1", sha256="53d9c791d60372a90a59709863570246066f395b9e83f0011865f930a53a63b4") + + depends_on("py-setuptools", type="build") + + depends_on("py-galaxy-util", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-galaxy-objectstore/package.py b/var/spack/repos/builtin/packages/py-galaxy-objectstore/package.py new file mode 100644 index 0000000000..ad007c8c76 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-galaxy-objectstore/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class PyGalaxyObjectstore(PythonPackage): + """The Galaxy object store framework and default implementations.""" + + homepage = "https://github.com/galaxyproject/galaxy" + pypi = "galaxy-objectstore/galaxy-objectstore-22.1.1.tar.gz" + + version("22.1.1", sha256="321a70f8bce89fec8d0322ba5821ee0b26d5cd3170a8dc9b7278cd383a9e88dd") + + depends_on("py-setuptools", type="build") + + depends_on("py-galaxy-util", type=("build", "run")) + depends_on("py-pyyaml", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-galaxy-tool-util/package.py b/var/spack/repos/builtin/packages/py-galaxy-tool-util/package.py new file mode 100644 index 0000000000..5b02cb236c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-galaxy-tool-util/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class PyGalaxyToolUtil(PythonPackage): + """The Galaxy tool utilities.""" + + homepage = "https://github.com/galaxyproject/galaxy" + pypi = "galaxy-tool-util/galaxy-tool-util-22.1.5.tar.gz" + + version("22.1.5", sha256="60e0372f16255c5c11ec5c49dff432ed3beb97123d026f463cf633bc605c0112") + + depends_on("py-setuptools", type="build") + + depends_on("py-galaxy-util@22.1:", type=("build", "run")) + depends_on("py-galaxy-containers@22.1:", type=("build", "run")) + depends_on("py-lxml", type=("build", "run")) + depends_on("py-pydantic", type=("build", "run")) + depends_on("py-pyyaml", type=("build", "run")) + depends_on("py-sortedcontainers", type=("build", "run")) + depends_on("py-typing-extensions", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-galaxy-util/package.py b/var/spack/repos/builtin/packages/py-galaxy-util/package.py new file mode 100644 index 0000000000..58828ed584 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-galaxy-util/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class PyGalaxyUtil(PythonPackage): + """Galaxy Generic Utilities""" + + homepage = "https://github.com/galaxyproject/galaxy" + pypi = "galaxy-util/galaxy-util-22.1.2.tar.gz" + + version("22.1.2", sha256="80257c94dc9122ebf80d643aa3962fe8beda23dbba8fc4820a0d2b720f479f98") + + depends_on("py-setuptools", type="build") + + depends_on("py-bleach", type=("build", "run")) + depends_on("py-boltons", type=("build", "run")) + depends_on("py-docutils", type=("build", "run")) + depends_on("py-importlib-resources", type=("build", "run")) + depends_on("py-markupsafe", type=("build", "run")) + depends_on("py-packaging@:21", type=("build", "run")) + depends_on("py-pycryptodome", type=("build", "run")) + depends_on("py-pyparsing", type=("build", "run")) + depends_on("py-pyyaml", type=("build", "run")) + depends_on("py-requests", type=("build", "run")) + depends_on("py-routes", type=("build", "run")) + depends_on("py-typing-extensions", type=("build", "run")) + depends_on("py-zipstream-new", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-poetry-plugin-export/package.py b/var/spack/repos/builtin/packages/py-poetry-plugin-export/package.py index 7a502000b1..1f4f74e476 100644 --- a/var/spack/repos/builtin/packages/py-poetry-plugin-export/package.py +++ b/var/spack/repos/builtin/packages/py-poetry-plugin-export/package.py @@ -15,5 +15,6 @@ class PyPoetryPluginExport(PythonPackage): version("1.0.7", sha256="f6ac707ae227b06b2481249ed2678ff6b810b3487cac0fbb66eb0dc2bfd6ecf1") depends_on("python@3.7:3", type=("build", "run")) - depends_on("py-poetry@1.2:1", type=("build", "run")) depends_on("py-poetry-core@1.1:1", type=("build", "run")) + + # depends_on("py-poetry@1.2:1", type="run") # circular dependency diff --git a/var/spack/repos/builtin/packages/py-pulsar-galaxy-lib/package.py b/var/spack/repos/builtin/packages/py-pulsar-galaxy-lib/package.py new file mode 100644 index 0000000000..bb1f833cfe --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pulsar-galaxy-lib/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack.package import * + + +class PyPulsarGalaxyLib(PythonPackage): + """Distributed job execution application built for Galaxy (http://galaxyproject.org/).""" + + homepage = "https://github.com/galaxyproject/pulsar" + pypi = "pulsar-galaxy-lib/pulsar-galaxy-lib-0.14.16.tar.gz" + + version("0.14.16", sha256="f3330350d2e85c7228cebf83f74fc4c0cc5e8e7557bb6e5ae55f5556d7e6fbff") + + depends_on("py-setuptools", type="build") + + depends_on("py-galaxy-job-metrics@19.9.0:", type=("build", "run")) + depends_on("py-galaxy-objectstore@19.9.0:", type=("build", "run")) + depends_on("py-galaxy-tool-util@19.9.0:", type=("build", "run")) + depends_on("py-galaxy-util@19.9.0:", type=("build", "run")) + depends_on("py-webob", type=("build", "run")) + depends_on("py-psutil", type=("build", "run")) + depends_on("py-pastedeploy", type=("build", "run")) + depends_on("py-pyyaml", type=("build", "run")) + depends_on("py-paramiko", type=("build", "run")) + depends_on("py-typing-extensions", type=("build", "run")) -- cgit v1.2.3-60-g2f50