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https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 10:24:38 +08:00
Daniel Blankenberg
5b1552ffa8
Add new bx-python eggs. Reorganize all MAF tools into a unified directory, and update tool_conf. Remember to update tool_conf.xml from one of the samples (tool_conf.xml.sample or tool_conf.xml.main).
38 lines
1.7 KiB
Python
38 lines
1.7 KiB
Python
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def load_maf_data( sep='\t' ):
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# FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
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# set data.name in exec_before_job().
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maf_sets = {}
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for line in open( "/depot/data2/galaxy/maf_index.loc" ):
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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fields = line.split( sep )
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#read each line, if not enough fields, go to next line
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try:
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maf_desc = fields[0]
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maf_uid = fields[1]
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builds = fields[2]
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build_list =[]
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split_builds = builds.split( "," )
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for build in split_builds:
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this_build = build.split( "=" )[0]
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build_list.append( this_build )
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paths = fields[3]
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maf_sets[ maf_uid ] = {}
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maf_sets[ maf_uid ][ 'description' ] = maf_desc
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maf_sets[ maf_uid ][ 'builds' ] = build_list
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except:
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continue
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return maf_sets
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def exec_before_job(app, inp_data, out_data, param_dict, tool):
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maf_sets = load_maf_data()
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if param_dict[ 'maf_source_type' ][ 'maf_source' ] == "cached":
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for name, data in out_data.items():
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try:
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data.name = data.name + " [" + maf_sets[ str( param_dict[ 'maf_source_type' ][ 'mafType' ] ) ][ 'description' ] + "]"
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except KeyError:
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data.name = data.name + " [unknown MAF source specified]"
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if param_dict[ 'summary' ].lower() == "true":
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for name, data in out_data.items():
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data.change_datatype( 'tabular' )
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