1 | # before running the qc, need to rename various output files
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2 | import os, string, time
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3 | from galaxy import datatypes
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4 | from galaxy import app
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5 | import galaxy.util
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6 |
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7 | #Provides Upload tool with access to list of available builds
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8 | repospath = '/usr/local/galaxy/data/rg'
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9 | builds = []
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10 | #Read build names and keys from galaxy.util
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11 | for dbkey, build_name in galaxy.util.dbnames:
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12 | builds.append((build_name,dbkey,False))
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13 |
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14 | def timenow():
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15 | """return current time as a string
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16 | """
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17 | return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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18 |
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19 | #Return available builds
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20 | def get_available_builds(defval='hg18'):
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21 | for i,x in enumerate(builds):
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22 | if x[1] == defval:
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23 | x = list(x)
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24 | x[2] = True
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25 | builds[i] = tuple(x)
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26 | return builds
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27 |
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28 | # Create link to files here
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29 | def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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30 | base_name = param_dict.get( 'title1', 'Null_Phenotype' )
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31 | base_name = base_name.encode()
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32 | info = 'Null phenotypes created by rgfakePhe at %s' % timenow()
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33 | s = string.whitespace + string.punctuation
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34 | ptran = string.maketrans(s,'_'*len(s))
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35 | base_name = base_name.translate(ptran)
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36 | data = out_data['ppheout']
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37 | data.name = '%s.phe' % (base_name) # that's how they've been named in rgfakePhe.py
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38 | data.file_name = data.file_name
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39 | data.metadata.base_name = base_name
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40 | out_data['pheout'] = data
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41 | app.model.context.flush()
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42 |
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43 |
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44 |
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45 |
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46 |
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