Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/planemo/mulled.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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"""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", )