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SHELL_API.md

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Linux Shell API

For more information about the dataset structure, please visit [Data set structure](./README.md) </br>
Syntax: RepositoryManager $COMMAND.  

Allowed Commands are :

  • RegisterUser

    To register the current user to the GMQL repository.

  • UnRegisterUser

    To unregister the current user from GMQL repository. All the datasets, history, User private schemata and user results will be deleted. The Samples on the Local File System will not be deleted.

  • CREATEDS DS_NAME SCHEMA_URL SAMPLES_PATH

    DS_NAME is the new dataset name

    SCHEMA_URL is the path to the schema file

      - The schema can be a keyword { BED | BEDGRAPH | NARROWPEAK | BROADPEAK }

    SAMPLES_PATH is the path to the samples, can be one of the following formats:

      - Samples urls comma separated: /to/the/path/sample1.bed,/to/the/path/sample2.bed 

  - Samples folder Path: /to/the/path/samplesFolder/ 
    in this case all the samples with an associated metadata will be added to the dataset.

    TIP: each sample file must be associated with a metadata file. The meta data file name should have the full name of the sample ended with ".meta" extension, for example: { sample.bed sample.bed.meta }

  • DELETEDS DS_NAME

    To Delete a dataset named DS_NAME

  • ADDSAMPLE DS_NAME SAMPLE_URL

    DS_NAME the dataset name (It has to be already added in the system).

    SAMPLE_URL is the path to the sample. No need to add the metadata Path since it must be in the same folder. For example: /to/the/path/sample.bed

  • DELETESAMPLE DS_NAME SAMPLE_URL

    Delete one sample form the dataset named DS_NAME

    SAMPLE_URL must be identical to what { LIST DS_NAME } command prints.

  • LIST ALL|DS_NAME

    ALL to print all the datasets for the current user and the public user.

    DS_NAME to print the samples of this dataset

  • CopyDSToLocal DS_NAME LOCAL_DIRECTORY

    This command copy all the samples of DS_NAME to local folder.
    The samples will be copied with its metadata.
    LOCAL_DIRECTORY is the full path to the local location.

INFO: For more information read the GMQL shell commands document.