Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/mulled.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Planemo specific utilities for dealing with mulled containers.
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2
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3 The extend galaxy-tool-util's features with planemo specific idioms.
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4 """
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5 from __future__ import absolute_import
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6
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7 import os
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8
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9 from galaxy.tool_util.deps.mulled.mulled_build import (
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10 DEFAULT_CHANNELS,
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11 ensure_installed,
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12 InvolucroContext,
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13 )
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14 from galaxy.tool_util.deps.mulled.util import build_target
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15
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16 from planemo.conda import collect_conda_target_lists
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17 from planemo.io import shell
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18
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19
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20 def conda_to_mulled_targets(conda_targets):
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21 return list(map(lambda c: build_target(c.package, c.version), conda_targets))
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22
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23
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24 def collect_mulled_target_lists(ctx, paths, recursive=False):
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25 return list(map(conda_to_mulled_targets, collect_conda_target_lists(ctx, paths, recursive=recursive)))
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26
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28 def build_involucro_context(ctx, **kwds):
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29 """Build a galaxy-tool-util InvolucroContext tailored to planemo use.
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30
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31 Using planemo's common command-line/global config options.
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32 """
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33 involucro_path_default = os.path.join(ctx.workspace, "involucro")
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34 involucro_path = kwds.get("involucro_path", involucro_path_default)
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35 use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
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36 shell_exec = shell if use_planemo_shell else None
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37 involucro_context = InvolucroContext(involucro_bin=involucro_path,
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38 shell_exec=shell_exec)
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39 if not ensure_installed(involucro_context, True):
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40 raise Exception("Failed to install involucro for Planemo.")
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41 return involucro_context
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42
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43
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44 def build_mull_target_kwds(ctx, **kwds):
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45 """Adapt Planemo's CLI and workspace configuration to galaxy-tool-util's mulled_build options."""
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46 involucro_context = build_involucro_context(ctx, **kwds)
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47 channels = kwds.get("conda_ensure_channels", ",".join(DEFAULT_CHANNELS))
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48 namespace = kwds.get("mulled_namespace", "biocontainers")
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49 target_kwds = {
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50 'involucro_context': involucro_context,
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51 'channels': channels.split(","),
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52 'namespace': namespace,
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53 'verbose': ctx.verbose,
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54 }
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55
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56 conda_version = kwds.get("mulled_conda_version", None)
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57 if conda_version is not None:
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58 target_kwds["conda_version"] = conda_version
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59 return target_kwds
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60
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61
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62 __all__ = (
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63 "build_involucro_context",
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64 "build_mull_target_kwds",
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65 "collect_mulled_target_lists",
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66 "conda_to_mulled_targets",
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67 )