[2] | 1 | import pkg_resources; pkg_resources.require( "bx-python" ) |
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| 2 | from bx.align import maf |
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| 3 | from galaxy import datatypes, config, jobs |
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| 4 | from shutil import move |
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| 5 | |
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| 6 | def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): |
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| 7 | output_data = out_data.items()[0][1] |
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| 8 | history = output_data.history |
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| 9 | if history == None: |
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| 10 | print "unknown history!" |
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| 11 | return |
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| 12 | new_stdout = "" |
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| 13 | split_stdout = stdout.split("\n") |
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| 14 | basic_name = output_data.name |
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| 15 | output_data_list = [] |
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| 16 | for line in split_stdout: |
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| 17 | if line.startswith("#FILE1"): |
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| 18 | fields = line.split("\t") |
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| 19 | dbkey = fields[1] |
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| 20 | filepath = fields[2] |
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| 21 | output_data.dbkey = dbkey |
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| 22 | output_data.name = basic_name + " (" + dbkey + ")" |
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| 23 | app.model.context.add( output_data ) |
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| 24 | app.model.context.flush() |
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| 25 | output_data_list.append(output_data) |
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| 26 | elif line.startswith("#FILE"): |
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| 27 | fields = line.split("\t") |
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| 28 | dbkey = fields[1] |
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| 29 | filepath = fields[2] |
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| 30 | newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) |
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| 31 | newdata.set_size() |
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| 32 | newdata.extension = "bed" |
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| 33 | newdata.name = basic_name + " (" + dbkey + ")" |
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| 34 | app.model.context.add( newdata ) |
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| 35 | app.model.context.flush() |
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| 36 | history.add_dataset( newdata ) |
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| 37 | app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset ) |
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| 38 | app.model.context.add( history ) |
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| 39 | app.model.context.flush() |
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| 40 | try: |
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| 41 | move(filepath,newdata.file_name) |
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| 42 | newdata.info = newdata.name |
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| 43 | newdata.state = newdata.states.OK |
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| 44 | except: |
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| 45 | newdata.info = "The requested file is missing from the system." |
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| 46 | newdata.state = newdata.states.ERROR |
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| 47 | newdata.dbkey = dbkey |
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| 48 | newdata.init_meta() |
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| 49 | newdata.set_meta() |
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| 50 | newdata.set_peek() |
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| 51 | app.model.context.flush() |
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| 52 | output_data_list.append(newdata) |
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| 53 | else: |
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| 54 | new_stdout = new_stdout + line |
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| 55 | for data in output_data_list: |
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| 56 | if data.state == data.states.OK: |
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| 57 | data.info = new_stdout |
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| 58 | app.model.context.add( data ) |
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| 59 | app.model.context.flush() |
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