Mercurial > repos > sanbi-uwc > data_manager_novoalign_license_uploader

annotate upload_novoalign_lic.py @ 0:0b64aa6d4214 draft

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planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
author sanbi-uwc
date Sun, 28 Feb 2016 14:51:11 -0500
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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2 # Zipho Masholoigu (SANBI-UWC)
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
diff changeset
4 import sys
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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5 import os
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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6 import tempfile
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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7 import shutil
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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8 import optparse
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
diff changeset
9 import urllib2
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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10 import subprocess
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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12 import logging
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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13 log = logging.getLogger( __name__ )
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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15 LICENCE_TARGET_DIRECTORY = "tool-data/novoalign/"
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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17 #Parse Command Line
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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18 parser = optparse.OptionParser()
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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19 args = parser.parse_args()
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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21 filename = args[0]
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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23 #read the contents of the license file
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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24 license_str = open( filename ).read()
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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26 #create the licence target directory
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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27 os.mkdir( LICENCE_TARGET_DIRECTORY )
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
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29 #save info to json file
0b64aa6d4214 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fdbfeddc2f83df93d20ce1e75193bb5a8db2524a
sanbi-uwc
parents:
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30 open( filename, 'wb' ).write( license_str )