Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo/mulled.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
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date | Mon, 01 Jun 2020 08:59:25 -0400 |
parents | 79f47841a781 |
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--- a/env/lib/python3.7/site-packages/planemo/mulled.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -"""Planemo specific utilities for dealing with mulled containers. - -The extend galaxy-tool-util's features with planemo specific idioms. -""" -from __future__ import absolute_import - -import os - -from galaxy.tool_util.deps.mulled.mulled_build import ( - DEFAULT_CHANNELS, - ensure_installed, - InvolucroContext, -) -from galaxy.tool_util.deps.mulled.util import build_target - -from planemo.conda import collect_conda_target_lists -from planemo.io import shell - - -def conda_to_mulled_targets(conda_targets): - return list(map(lambda c: build_target(c.package, c.version), conda_targets)) - - -def collect_mulled_target_lists(ctx, paths, recursive=False): - return list(map(conda_to_mulled_targets, collect_conda_target_lists(ctx, paths, recursive=recursive))) - - -def build_involucro_context(ctx, **kwds): - """Build a galaxy-tool-util InvolucroContext tailored to planemo use. - - Using planemo's common command-line/global config options. - """ - involucro_path_default = os.path.join(ctx.workspace, "involucro") - involucro_path = kwds.get("involucro_path", involucro_path_default) - use_planemo_shell = kwds.get("use_planemo_shell_exec", True) - shell_exec = shell if use_planemo_shell else None - involucro_context = InvolucroContext(involucro_bin=involucro_path, - shell_exec=shell_exec) - if not ensure_installed(involucro_context, True): - raise Exception("Failed to install involucro for Planemo.") - return involucro_context - - -def build_mull_target_kwds(ctx, **kwds): - """Adapt Planemo's CLI and workspace configuration to galaxy-tool-util's mulled_build options.""" - involucro_context = build_involucro_context(ctx, **kwds) - channels = kwds.get("conda_ensure_channels", ",".join(DEFAULT_CHANNELS)) - namespace = kwds.get("mulled_namespace", "biocontainers") - target_kwds = { - 'involucro_context': involucro_context, - 'channels': channels.split(","), - 'namespace': namespace, - 'verbose': ctx.verbose, - } - - conda_version = kwds.get("mulled_conda_version", None) - if conda_version is not None: - target_kwds["conda_version"] = conda_version - return target_kwds - - -__all__ = ( - "build_involucro_context", - "build_mull_target_kwds", - "collect_mulled_target_lists", - "conda_to_mulled_targets", -)