Metadata-Version: 1.1
Name: pyega3
Version: 3.0.28
Summary: EGA python client
Home-page: https://github.com/EGA-archive/ega-download-client
Author: EGA team
Author-email: ega-helpdesk@ebi.ac.uk
License: Apache License, Version 2.0
Description: EGA python client - pyEGA3
        pyEGA3 uses the EGA REST API to download authorized datasets and files
        
        Currently works only with Python3
        
        REQUIREMENTS:
        Python "requests" module
        http://docs.python-requests.org/en/master/
        pip3 install requests
        
        Firewall Ports
        This client makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443/) and to the EGA Data API (https://ega.ebi.ac.uk:8051). Both ports 8443 and 8051 must be reachable from the location where this client script is run. Otherwise you will experience timeouts.
        (e.g. https://ega.ebi.ac.uk:8443/ega-openid-connect-server/, https://ega.ebi.ac.uk:8051/elixir/central/stats/load should not time out).
        ----------------------------------------------------------------------------------
        INSTALLATION via Pip:
        sudo pip3 install pyega3
        ----------------------------------------------------------------------------------
        INSTALLATION via Conda(Bioconda channel):
        conda config --add channels bioconda
        conda install pyega3
        ----------------------------------------------------------------------------------
        USAGE:
        pyega3 [-h] [-d] -cf CREDENTIALS_FILE [-c CONNECTIONS] {datasets,files,fetch} ...
        
        Download from EMBL EBI's EGA (European Genome-phenome Archive)
        
        positional arguments:
          {datasets,files,fetch}
                                subcommands
            datasets            List authorized datasets
            files               List files in a specified dataset
            fetch               Fetch a dataset or file
        
        optional arguments:
          -h, --help            show this help message and exit
          -d, --debug           Extra debugging messages
          -cf CREDENTIALS_FILE, --credentials-file CREDENTIALS_FILE
                                JSON file containing credentials
                                e.g.{'username':'user1','password':'toor'}
          -c CONNECTIONS, --connections CONNECTIONS
                                Download using specified number of connections                      
                                
        ----------------------------------------------------------------------------------
          
        Credentials file supposed to be in json format e.g:
        {
            "username": "my.email@domain.edu",
            "password": "mypassword",    
            "client_secret":"AMenuDLjVdVo4BSwi0QD54LL6NeVDEZRzEQUJ7hJOM3g4imDZBHHX0hNfKHPeQIGkskhtCmqAJtt_jm7EKq-rWw"
        }
        
        Your username and password are provided to you by EGA.
        Specifying password is not mandatory - if password is not provided 
        the user will be asked to enter it from the console
        
        ----------------------------------------------------------------------------------
        
        Parallelism ( download via multiple connections ) works on the file level, 
        but still usable while downloading whole dataset. 
        If -c command line switch is provided all big files (>100Mb) in the 
        dataset will be downloaded using specified # of connections.
        
        The number of connections breaks down individual file downloads into segments, 
        which are then downloaded in parallel. So using a very high number actually 
        introduces overhead that slows down the download of the file.
        Files are still downloaded in sequence – so multiple connections doesn't mean 
        downloading multiple files in parallel, if an entire dataset is being downloaded.
        
        ----------------------------------------------------------------------------------
        
        GENOMIC RANGE REQUESTS ( via Htsget protocol ) :
        
        usage: pyega3 fetch [-h] [--reference-name REFERENCE_NAME]
                            [--reference-md5 REFERENCE_MD5] [--start START]
                            [--end END] [--format {BAM,CRAM}] [--saveto [SAVETO]]
                            identifier
        
        positional arguments:
          identifier            Id for dataset (e.g. EGAD00000000001) or file (e.g.
                                EGAF12345678901)
        
        optional arguments:
          -h, --help            show this help message and exit
          --reference-name REFERENCE_NAME, -r REFERENCE_NAME
                                The reference sequence name, for example 'chr1', '1',
                                or 'chrX'. If unspecified, all data is returned.
          --reference-md5 REFERENCE_MD5, -m REFERENCE_MD5
                                The MD5 checksum uniquely representing the requested
                                reference sequence as a lower-case hexadecimal string,
                                calculated as the MD5 of the upper-case sequence
                                excluding all whitespace characters.
          --start START, -s START
                                The start position of the range on the reference,
                                0-based, inclusive. If specified, reference-name or
                                reference-md5 must also be specified.
          --end END, -e END     The end position of the range on the reference,
                                0-based exclusive. If specified, reference-name or
                                reference-md5 must also be specified.
          --format {BAM,CRAM}, -f {BAM,CRAM}
                                The format of data to request.
          --saveto [SAVETO]     Output file(for files)/output dir(for datasets)
        
        
        
Keywords: EGA,archive
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.4
