Up: Component summary
Up: Component summary
Component
CGHubDownloadExecutes 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 |
Inputs| 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. |
Outputs| 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! |
Parameters| 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. |