Use basespace CLI to download run data #13
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The old method of downloading data created a directory within the run directory, which is different than this current method. We need to ensure that we can still demux the data. This may involve changing the demux scripts with the updated directory structure. The contents of the directories are the same. New download app: $ tree new_method -L 1
new_method
├── <run_id>.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
7 directories, 11 filesOld download app: $ tree old_method -L 2
old_method
├──<run_id>
│ ├── 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 |
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After some more investigation, this does not cause any issues with the demux app. Now instead of running the following: singularity run \
-B $resource_dir:/opt/resources -B $run_dir:/opt/analysis -B $bcl_dir:/opt/data \
miptools.sif --app demux -s $sample_list -p $platformwhere singularity run \
-B $resource_dir:/opt/resources -B $run_dir:/opt/analysis -B $run_dir:/opt/data \
miptools.sif --app demux -s $sample_list -p $platformWe will get the same output. We may additionally want to consider slightly changing the demux script so that we no longer need to bind |
This PR replaces the old python script for downloading data from the Illumina BaseSpace Sequence Hub.
Resolves #8