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Executes CGHub's GeneTorrent package's utilities. First, cgquery is used to query Analysis from CGHub. Then gtdownload is used to download all relevant aliquots e.g. samples.

Version 0.1
Bundle sequencing
Categories External
Authors Lauri Lyly (lauri.lyly@helsinki.fi)
Issue tracker View/Report issues
Requires GeneTorrent
Source files component.xml main.bash
Usage Example with default values


Name Type Mandatory Description
key BinaryFile Mandatory Credential file to use when attempting to communicate with CGHub.
analysisIds CSV Optional Instead of querying, pick UUIDs of analysis sets from the "analysis_id" column of this file.


Name Type Description
queryResults TextFile Text file output by cgquery, containing the analysis annotations.
queryResultCSV CSV Text file output by cgquery, containing the analysis annotations.
data BinaryFolder Folder containing the data sets. Notice that this will be huge!


Name Type Default Description
cgquery string (no default) Query as in: https://cghub.ucsc.edu/docs/user/query.html . For example, disease_abbr=SKCM&library_strategy=(RNA-Seq)&platform=ILLUMINA
cgqueryOptions string "" Options expanded to the cgquery command line.
gtdownloadOptions string "" Options expanded to the gtdownload command line.
outputLocation string "" If non-empty, the results are downloaded here. If a dataset exists, it is not downloaded again.
queryOnly boolean false Set true to query only. Output folder will be empty.

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