Use basespace CLI in download app#25
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The output folder structure now reflects the output folder structure of the superseded app
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Below we provide a comparison of the output directory file structure. The file structure is almost identical with the only differences being a Superseded app: new_download_app
└── 214264108
├── 210923_214264108.json
├── Config
├── Data
├── InstrumentAnalyticsLogs
├── InterOp
├── Logs
├── Recipe
├── RTAComplete.txt
├── RTAConfiguration.xml
├── RTALogs
├── RTARead1Complete.txt
├── RTARead2Complete.txt
├── RTARead3Complete.txt
├── RTARead4Complete.txt
├── RunCompletionStatus.xml
├── RunInfo.xml
├── RunParameters.xml
└── SampleSheet.csv
8 directories, 11 filesNew download app: superseded_download_app
├── 214264108
│ ├── Config
│ ├── Data
│ ├── InstrumentAnalyticsLogs
│ ├── InterOp
│ ├── Logs
│ ├── Recipe
│ ├── RTAComplete.txt
│ ├── RTAConfiguration.xml
│ ├── RTALogs
│ ├── RTARead1Complete.txt
│ ├── RTARead2Complete.txt
│ ├── RTARead3Complete.txt
│ ├── RTARead4Complete.txt
│ ├── RunCompletionStatus.xml
│ ├── RunInfo.xml
│ ├── RunParameters.xml
│ └── SampleSheet.csv
└── nohup.out
8 directories, 11 files |
arisp99
commented
Feb 25, 2022
| scp /opt/programs/parasight_v7.6/parasight.pl /opt/bin/parasight76.pl | ||
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| # install basespace cli | ||
| BS_PATH="https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs" |
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Instead of downloading the latest version of the CLI tool, we can specify the version number by replacing latest with a version number. The available versions can be found here.
arisp99
commented
Feb 25, 2022
Checks if `run_id` is unset and writes the help page to `stderr`.
aydemiro
reviewed
Feb 28, 2022
aydemiro
reviewed
Feb 28, 2022
aydemiro
reviewed
Feb 28, 2022
aydemiro
reviewed
Feb 28, 2022
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This PR creates a new basespace download app that uses the official basespace CLI. This PR supersedes the work in #13 and introduces one large change. Namely, in order to maintain backward compatibility, we supersede the original download app that uses a python script for downloading data. Users may, therefore, still use the old download app.
Closes #8.