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This particular pipeline requires a bowtie index and an annotation model:

Image RemovedImage Added

The request to launch the pipeline needs to specify one resource ID for each input.

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wget -q -O - "http://localhost:8080/flow/api/v1/library_files/list${AUTHDETAILS}&assembly=hg19" |  python -m json.tool | gvim -

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[
    {
        "annotationModel": "",
        "assembly": "hg19",
        "description": "Reference sequence",
        "fileType": "Genome sequence",
        "id": 100
    },
    {
        "annotationModel": "",
        "assembly": "hg19",
        "description": "Cytoband",
        "fileType": "cytoBand.txt",
        "id": 101
    },
    {
        "annotationModel": "",
        "assembly": "hg19",
        "description": "Bowtie index",
        "fileType": "Bowtie Index",
        "id": 102
    },
    {
        "annotationModel": "hg19_refseq_15_05_07_v2",
        "assembly": "hg19",
        "description": "Annotation file: hg19_refseq_15_05_07_v2",
        "fileType": "Annotation model",
        "id": 103
    }
]

The pipeline can be launched in any project using RunPython.py

python RunPipeline.py  -v --server http://localhost:8080 --user admin --password $FLOW_TOKEN --project_id 0 --pipeline AlignAndQuantify --inputs 102,103,102 

This action will cause two tasks to start running:

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python UploadSamples.py -v --server http://localhost:8080 --user admin --password $FLOW_TOKEN --files ~/sampleA.fastq.gz ~/sampleB.fastq.gz --project NewProject --pipeline AlignAndQuantify --inputs 102,103,102

Add a collaborator to a project

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Monitor a folder and upload files as they are created

#!/bin/bash
inotifywait -m $PATH_TO_MONITOR -e create -e moved_to |
  while read path action file; do
      if [[ $file == *.fastq.gz ]]; then
              echo "Uploading $file"
              python UploadSamples.py -v --server $SERVER --user $USER --password $TOKEN --files $path/$file --project "$PROJECT" 
      fi
  done

Monitor the queue and send a notification if there are too many waiting tasks

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Code Block
language bash
#!/bin/bash while true; do result=`python QueueStatistics.py --server $SERVER --user $USER --password $TOKEN --max_waiting $MAX_WAITING` if [ $? -eq 1 ]; then /usr/bin/notify-send $result exit 1 fi sleep $INTERVAL done

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