annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """
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2 Backup resolvers for when dependencies can not be loaded from the database.
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3 Mainly suited for testing stage.
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4
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5 Ideally all dependencies will be stored in the database
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6 when a tool is added from a Tool Shed.
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7
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8 That should remain the preferred way of locating dependencies.
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9
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10 In cases where that is not possible
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11 for example during testing this resolver can act as a backup.
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12
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13 This resolver looks not just for manually added dependencies
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14 but also ones added from a Tool Shed.
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15
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16 This tool is still under development so the default behaviour could change.
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17 It has been tested when placed in the same directory as galaxy_packages.py
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18
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19 At the time of writing July 3 2015 this resolver has to be plugged in.
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20 See bottom for instructions on how to add this resolver.
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21
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22 """
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23 import logging
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24 from os import listdir
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25 from os.path import (
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26 exists,
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27 getmtime,
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28 join
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29 )
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30
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31 from . import (
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32 Dependency,
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33 NullDependency
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34 )
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35 from .galaxy_packages import BaseGalaxyPackageDependencyResolver
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36
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37 log = logging.getLogger(__name__)
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38
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39 MANUAL = "manual"
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40 PREFERRED_OWNERS = MANUAL + ",iuc,devteam"
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41
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42
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43 class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver):
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44 dict_collection_visible_keys = BaseGalaxyPackageDependencyResolver.dict_collection_visible_keys + ['preferred_owners', 'select_by_owner']
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45 resolver_type = "unlinked_tool_shed_packages"
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46
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47 def __init__(self, dependency_manager, **kwds):
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48 super().__init__(dependency_manager, **kwds)
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49 # Provide a list of preferred owners whose dependency to use
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50 self.preferred_owners = kwds.get('preferred_owners', PREFERRED_OWNERS).split(",")
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51 # Option to ignore owner and just use last modified time
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52 self.select_by_owner = str(kwds.get('select_by_owner', "true")).lower() != "false"
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53
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54 def _find_dep_versioned(self, name, version, type='package', **kwds):
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55 try:
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56 possibles = self._find_possible_dependencies(name, version, type)
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57 if len(possibles) == 0:
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58 log.debug("Unable to find dependency,'%s' '%s' '%s'", name, version, type)
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59 return NullDependency(version=version, name=name)
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60 elif len(possibles) == 1:
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61 # Only one candidate found so ignore any preference rules
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62 return possibles[0].dependency
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63 else:
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64 # Pick the preferred one
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65 return self._select_preferred_dependency(possibles).dependency
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66 except Exception:
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67 log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type)
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68 return NullDependency(version=version, name=name)
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69
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70 # Finds all possible dependency to use
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71 # Should be extended as required
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72 # Returns CandidateDependency objects with data for preference picking
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73 def _find_possible_dependencies(self, name, version, type):
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74 possibles = []
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75 if exists(self.base_path):
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76 path = join(self.base_path, name, version)
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77 if exists(path):
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78 # First try the way without owner/name/revision
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79 package = self._galaxy_package_dep(path, version, name, type, True)
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80 if not isinstance(package, NullDependency):
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81 log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, path)
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82 possibles.append(CandidateDependency(package, path))
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83 # now try with an owner/name/revision
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84 for owner in listdir(path):
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85 owner_path = join(path, owner)
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86 for package_name in listdir(owner_path):
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87 if package_name.lower().startswith("package_" + name.lower()):
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88 package_path = join(owner_path, package_name)
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89 for revision in listdir(package_path):
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90 revision_path = join(package_path, revision)
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91 package = self._galaxy_package_dep(revision_path, version, name, type, True)
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92 if not isinstance(package, NullDependency):
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93 log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path)
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94 possibles.append(CandidateDependency(package, package_path, owner))
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95 return possibles
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96
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97 def _select_preferred_dependency(self, possibles, by_owner=None):
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98 if by_owner is None:
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99 by_owner = self.select_by_owner
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100 preferred = []
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101 if by_owner:
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102 for owner in self.preferred_owners:
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103 for candidate in possibles:
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104 if candidate.owner == owner:
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105 preferred.append(candidate)
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106 if len(preferred) == 1:
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107 log.debug("Picked dependency based on owner '%s'", owner)
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108 return preferred[0]
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109 elif len(preferred) > 1:
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110 log.debug("Multiple dependency found with owner '%s'", owner)
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111 break
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112 if len(preferred) == 0:
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113 preferred = possibles
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114 latest_modified = 0
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115 for candidate in preferred:
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116 modified = getmtime(candidate.path)
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117 if latest_modified < modified:
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118 latest_candidate = candidate
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119 latest_modified = modified
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120 log.debug("Picking dependency at '%s' as it was the last modified", latest_candidate.path)
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121 return latest_candidate
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122
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123 """
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124 #Currently no need has been found for expand the verionsless method
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125 #This is an example of how it could be done
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126 def _find_dep_default( self, name, type='package', **kwds ):
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127 try:
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128 possibles = TODO
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129 if len(possibles) == 0:
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130 log.debug("Unable to find dependency,'%s' default '%s'", name, type)
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131 return NullDependency(version=None, name=name)
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132 elif len(possibles) == 1:
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133 #Only one candidate found so ignore any preference rules
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134 return possibles[0].dependency
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135 else:
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136 #Pick the preferred one
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137 return self._select_preferred_dependency(possibles, by_owner=False).dependency
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138 except Exception:
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139 log.exception("Unexpected error hunting for dependency '%s' default '%s'", name, type)
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140 return NullDependency(version=None, name=name)
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141 """
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142
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143
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144 class CandidateDependency(Dependency):
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145 dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['dependency', 'path', 'owner']
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146 dependency_type = 'unlinked_tool_shed_package'
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147
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148 @property
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149 def exact(self):
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150 return self.dependency.exact
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151
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152 def __init__(self, dependency, path, owner=MANUAL):
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153 self.dependency = dependency
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154 self.path = path
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155 self.owner = owner
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156
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157 def shell_commands(self):
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158 """
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159 Return shell commands to enable this dependency.
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160 """
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161 return self.dependency.shell_commands()
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162
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163
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164 __all__ = ('UnlinkedToolShedPackageDependencyResolver', )
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165
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166 """
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167 At the time of writing July 3 2015 this resolver has to be plugged in.
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168
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169 Adding resolver instructions:
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170
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171 1. create a dependency_resolvers_config.xml file
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172 <dependency_resolvers>
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173 <tool_shed_packages />
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174 <galaxy_packages />
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175 <galaxy_packages versionless="true" />
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176 <unlinked_tool_shed_packages />
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177 </dependency_resolvers>
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178
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179
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180 1a. ALWAYS add <tool_shed_packages /> first!!!!
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181
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182 1b. <galaxy_packages /> is optional as
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183 this resolver will also find dependency found by that resolver
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184 1bi Current default is to use a dependency to find that way first!
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185 1bii So an alternative version of dependency_resolvers_config.xml
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186 <dependency_resolvers>
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187 <tool_shed_packages />
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188 <unlinked_tool_shed_packages />
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189 <unlinked_tool_shed_packages versionless="true" />
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190 </dependency_resolvers>
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191
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192 1c. See __init__ for optional config values
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193 1ci versionless currently is handled by the super class
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194 GalaxyPackageDependencyResolver
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195
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196 2. Add a parameter to config.ini
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197 dependency_resolvers_config_file = ./config/dependency_resolvers_config.xml
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198
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199 2a. File name/path can be different
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200 2b. config key must be dependency_resolvers_config_file
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201
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202 3. For planemo it may be required to specify:
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203 --dependency_resolvers_config_file (xml file described in 1 above)
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204 --tool_dependency_dir (root of dependencies typically galaxy/dependency_dir)
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205 See planemo test --help for more information
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206 """