Mercurial > repos > iuc > data_manager_gemini_database_downloader
annotate data_manager/data_manager_gemini_download.py @ 3:172815da3d41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
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date | Tue, 04 Apr 2017 18:09:05 -0400 |
parents | 345412d58d75 |
children | fe5a9a7d95b0 |
rev | line source |
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0 | 1 #!/usr/bin/env python |
2 | |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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3 import datetime |
0 | 4 import json |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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5 import os |
0 | 6 import subprocess |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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7 import sys |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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8 |
0 | 9 |
10 def main(): | |
11 today = datetime.date.today() | |
12 params = json.loads( open( sys.argv[1] ).read() ) | |
13 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
14 os.mkdir( target_directory ) | |
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345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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0
diff
changeset
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15 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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16 subprocess.check_call( cmd, shell=True ) |
2
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
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17 data_manager_dict = { |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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18 'data_tables': { |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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19 'gemini_databases': [ |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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20 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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21 ] |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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22 } |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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23 } |
0 | 24 |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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25 # save info to json file |
0 | 26 with open( sys.argv[1], 'wb' ) as out: |
27 out.write( json.dumps( data_manager_dict ) ) | |
28 | |
3
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
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29 |
0 | 30 if __name__ == "__main__": |
31 main() |