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 <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* 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 <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-requests-cache/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* 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 <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pebble/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-gunicorn/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-parsley/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-paste/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-paste/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* 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 <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-lagom/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-supervisor/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-social-auth-core/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* 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 <ajstewart426@gmail.com>

* fix in py-poetry-plugin-export

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

8 files changed, 199 insertions, 1 deletions

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"))