Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/conda_recipes.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 conda recipe generation.
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2 """
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3
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4 from __future__ import absolute_import
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5
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6 import os
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7
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8 from planemo import git
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9 from planemo.bioconda_scripts import bioconductor_skeleton
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10 from planemo.io import info
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11
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12 # Bioconda helper functions
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13
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14
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15 def clone_bioconda_repo(path):
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16 """Clone bioconda repository in given path."""
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17 bioconda_repo = "git@github.com:bioconda/bioconda-recipes.git"
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18 git.clone(None, bioconda_repo, path)
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19 return "git clone of bioconda repo worked"
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20
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21
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22 def write_bioconda_recipe(package_name, clone, update, bioconda_dir_path=None):
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23 """Make a bioconda recipe given the package name.
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24
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25 clone: y/N , clone the whole bioconda repository and create recipe inside
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26 repository.
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27
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28 update: The update feature differs from the one in bioconda, as it
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29 updates the specific package, as opposed to the every package in the
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30 biocoda repository.
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31 """
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32 # set bioconda path
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33 if bioconda_dir_path is None:
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34 bioconda_recipe_path = os.path.join(os.path.expanduser("~"), "bioconda-recipes")
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35 else:
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36 bioconda_recipe_path = os.path.join(bioconda_dir_path, "bioconda-recipes")
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37
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38 # Clone
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39 if clone and (not os.path.exists(bioconda_recipe_path)):
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40 clone_bioconda_repo(bioconda_recipe_path)
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41 info("bioconda-recipes cloned and writing to %s" % bioconda_dir_path)
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42 else:
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43 info("Bioconda repository not cloned or already exists")
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44
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45 # Check if package_name is in recipes
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46 presence = any(package_name in r for r, d, f in os.walk(bioconda_recipe_path))
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47 if presence:
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48 info("Package already exists in bioconda")
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49 if update:
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50 info("Package will be updated")
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51 recipe_dir = os.path.join(bioconda_recipe_path, "recipes")
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52 bioconductor_skeleton.write_recipe(package_name, recipe_dir, True)
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53 elif not presence:
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54 info("Package found in bioconda recipes")
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55 recipe_dir = os.path.join(bioconda_recipe_path, "recipes")
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56 bioconductor_skeleton.write_recipe(package_name, recipe_dir, True)
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57 return
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58
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59
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60 __all__ = (
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61 "clone_bioconda_repo",
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62 "write_bioconda_recipe",
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63 )