Mercurial > repos > sanbi-uwc > data_manager_novoalign_license_uploader

annotate data_manager/novoalign_license_uploader.py @ 6:23915ef5be9d draft

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planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit fde5ecd26b6d6dd50bc7c4cb4201eb1a4068d8ed
author sanbi-uwc
date Mon, 29 Feb 2016 07:38:44 -0500
parents d8c61b89caf2
children
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d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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2 # Zipho Masholoigu (SANBI-UWC)
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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3
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
diff changeset
4 import os
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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5 import argparse
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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6
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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7 import logging
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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8 log = logging.getLogger( __name__ )
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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9
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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10 LICENSE_TARGET_DIRECTORY = "novoalign"
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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12 #Parse Command Line
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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13 parser = argparse.ArgumentParser(description="Upload the nonoalign license to the tool-data path")
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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14 parser.add_argument('--license_filename')
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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15 parser.add_argument('--license_dir')
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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16
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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17 args = parser.parse_args()
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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18 filename = args.license_filename
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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19
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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20 #create the license target directory
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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21 target_dir = args.license_dir + "/" + LICENSE_TARGET_DIRECTORY
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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22 license_file = target_dir+"/"+"license.lic"
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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23 if not os.path.isfile(license_file):
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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24 os.mkdir( target_dir )
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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25 #move/copy license file to the tool-data path
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
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26 os.rename( filename, target_dir+"/"+"license.lic")
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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27 else:
d8c61b89caf2 planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit bbe707e24f0baca8840603b0abb05bde8fa6d6a4
sanbi-uwc
parents:
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28 log.debug("License for novoalign seems to exists already")