Mercurial > repos > yating-l > jbrowsearchivecreator

annotate TrackHub.py @ 25:31a41ce128cc draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
author yating-l
date Fri, 13 Oct 2017 12:44:31 -0400
parents bb6fdccef474
children 127037c49bc8
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1 #!/usr/bin/env python
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3 import os
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4 import subprocess
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5 import shutil
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6 import zipfile
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7 import json
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8 import tempfile
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9 import logging
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11 from datatypes.Datatype import Datatype
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12 from apollo.ApolloInstance import ApolloInstance
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13 from tracks.TrackStyles import TrackStyles
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14 from util import subtools
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15 from util import santitizer
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18 class TrackHub:
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19 def __init__(self, inputFastaFile, apollo_user, outputFile, extra_files_path, tool_directory, trackType, apollo_host):
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21 self.rootAssemblyHub = None
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23 self.mySpecieFolderPath = None
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25 # Store intermediate files, will be removed if not in debug mode
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26 self.myTracksFolderPath = None
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28 # Store binary files: Bam, BigWig
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29 self.myBinaryFolderPath = None
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31 self.tool_directory = tool_directory
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32 self.trackType = trackType
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33 self.reference_genome = inputFastaFile
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34 self.genome_name = inputFastaFile.assembly_id
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35 self.extra_files_path = extra_files_path
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36 self.outputFile = outputFile
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37 self.chromSizesFile = None
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39 # Set up apollo
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40 self.apollo = ApolloInstance(apollo_host)
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41 self.apollo_user = apollo_user
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43 # Set all the missing variables of this class, and create physically the folders/files
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44 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
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45 # Init the Datatype
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46 Datatype.pre_init(self.reference_genome, self.chromSizesFile,
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47 self.extra_files_path, self.tool_directory,
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48 self.mySpecieFolderPath, self.myTracksFolderPath, self.myBinaryFolderPath, self.trackType)
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50 self._prepareRefseq()
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51 self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json")
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52 self._createTrackList()
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54 self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
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55 #self.cssFolderPath = os.path.join(self.mySpecieFolderPath, 'css')
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56 #self.cssFilePath = os.path.join(self.cssFolderPath, 'custom_track_styles.css')
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57 self.logger = logging.getLogger(__name__)
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58
0
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59
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61 def addTrack(self, trackDbObject):
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62 if trackDbObject['dataType'].lower() == 'bam':
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63 #new_track = subprocess.Popen(['echo', trackDbObject['options']], stdout=subprocess.PIPE)
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64 #subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
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65 subtools.add_track_json(self.trackList, trackDbObject['options'])
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66 #subtools.add_track_json(self.trackList, trackDbObject['track_json'])
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67 elif trackDbObject['dataType'].lower() == 'bigwig':
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68 subtools.add_track_json(self.trackList, trackDbObject['options'])
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69 else:
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70 if trackDbObject['trackType'] == 'HTMLFeatures':
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71 self._customizeHTMLFeature(trackDbObject)
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72 subtools.flatfile_to_json(trackDbObject['trackDataURL'], trackDbObject['dataType'], trackDbObject['trackType'], trackDbObject['trackLabel'], self.mySpecieFolderPath, trackDbObject['options'])
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75 def terminate(self, debug=False):
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76 """ Write html file """
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77 self._indexName()
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78 if not debug:
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79 self._removeRaw()
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80 self._makeArchive()
0
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81 print "Success!\n"
25
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83
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84 def _customizeHTMLFeature(self, trackDbObject):
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85 if trackDbObject['options']:
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86 subfeatures = trackDbObject['options'].get('subfeatureClasses')
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87 feature_color = trackDbObject['options']['feature_color']
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88 if subfeatures:
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89 for key, value in subfeatures.items():
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90 self.myTrackStyle.addCustomColor(value, feature_color)
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91 else:
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92 customizedFeature = santitizer.sanitize_name(trackDbObject['trackLabel'])
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93 clientConfig = json.loads(trackDbObject['options']['clientConfig'])
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94 clientConfig['renderClassName'] = customizedFeature
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95 trackDbObject['options']['clientConfig'] = json.dumps(clientConfig)
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96 self.myTrackStyle.addCustomColor(customizedFeature, feature_color)
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97
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98 def _removeRaw(self):
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99 if os.path.exists(self.myTracksFolderPath):
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100 shutil.rmtree(self.myTracksFolderPath)
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101
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102 def _createTrackList(self):
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103 if not os.path.exists(self.trackList):
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104 os.mknod(self.trackList)
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105
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106 def _prepareRefseq(self):
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107 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
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108 #try:
0
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109 #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
25
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110 #subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference_genome.false_path, '--out', self.mySpecieFolderPath])
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111 #except OSError as e:
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112 #print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
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113
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114 def _indexName(self):
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115 #subprocess.call(['generate-names.pl', '-v', '--out', self.mySpecieFolderPath])
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116 subtools.generate_names(self.mySpecieFolderPath)
0
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117 print "finished name index \n"
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118
25
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119 def _outHtml(self, host_name):
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120 with open(self.outputFile, 'w') as htmlfile:
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121 htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name
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122 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
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123 htmlstr += jbrowse_hub
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124 htmlfile.write(htmlstr)
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125
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126 def _makeArchive(self):
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127 self.apollo.loadHubToApollo(self.apollo_user, self.genome_name, self.mySpecieFolderPath, admin=True)
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128 apollo_host = self.apollo.getHost()
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129 self._outHtml(apollo_host)
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130
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131
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132 def __createAssemblyHub__(self, extra_files_path):
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133 # Get all necessaries infos first
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134 # 2bit file creation from input fasta
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135
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136 # baseNameFasta = os.path.basename(fasta_file_name)
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137 # suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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138 # nameTwoBit = suffixTwoBit + '.2bit'
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139 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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140 subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)
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141
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142 # Generate the twoBitInfo
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143 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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144 subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)
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145
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146 # Then we get the output to generate the chromSizes
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147 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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148 subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)
0
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149
25
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150 # We can get the biggest scaffold here, with chromSizesFile
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151 with open(self.chromSizesFile.name, 'r') as chrom_sizes:
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152 # TODO: Check if exists
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153 self.default_pos = chrom_sizes.readline().split()[0]
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154
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155 # TODO: Manage to put every fill Function in a file dedicated for reading reasons
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156 # Create the root directory
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157 myHubPath = os.path.join(extra_files_path, "myHub")
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158 if not os.path.exists(myHubPath):
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159 os.makedirs(myHubPath)
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160
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161 # Create the specie folder
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162 # TODO: Generate the name depending on the specie
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163 mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
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164 if not os.path.exists(mySpecieFolderPath):
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165 os.makedirs(mySpecieFolderPath)
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166 self.mySpecieFolderPath = mySpecieFolderPath
0
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167
25
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168 # We create the 2bit file while we just created the specie folder
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169 #self.twoBitName = self.genome_name + ".2bit"
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170 #self.two_bit_final_path = os.path.join(self.mySpecieFolderPath, self.twoBitName)
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171 #shutil.copyfile(twoBitFile.name, self.two_bit_final_path)
0
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172
25
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173 # Create the folder tracks into the specie folder
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174 tracksFolderPath = os.path.join(mySpecieFolderPath, "raw")
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175 if not os.path.exists(tracksFolderPath):
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176 os.makedirs(tracksFolderPath)
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177 self.myTracksFolderPath = tracksFolderPath
0
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178
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents: 24
diff changeset
179 myBinaryFolderPath = os.path.join(mySpecieFolderPath, 'bbi')
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents: 24
diff changeset
180 if not os.path.exists(myBinaryFolderPath):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents: 24
diff changeset
181 os.makedirs(myBinaryFolderPath)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents: 24
diff changeset
182 self.myBinaryFolderPath = myBinaryFolderPath
0
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
183
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents: 24
diff changeset
184 return myHubPath