{"id":2192,"date":"2016-12-12T14:50:24","date_gmt":"2016-12-12T12:50:24","guid":{"rendered":"http:\/\/bioinfo2.ugr.es\/MethFlow\/?page_id=2192"},"modified":"2016-12-16T10:58:17","modified_gmt":"2016-12-16T08:58:17","slug":"quick-start","status":"publish","type":"page","link":"https:\/\/bioinfo2.ugr.es\/MethFlow\/quick-start\/","title":{"rendered":"Quick start"},"content":{"rendered":"

Quick start is thought to try MethFlow without going into details and using the MethFlow virtual machine. For further information, see<\/span>\u00a0<\/span>the<\/span>\u00a0reference manual<\/a><\/span>.<\/span><\/p>\n

Install MethFlowVM<\/sup><\/h3>\n
    \n
  1. Install VirtualBox<\/a>.<\/li>\n
  2. Install VirtualBox Extension Pack<\/a>.<\/li>\n
  3. Download MethFlowVM<\/sup><\/a>\u00a0(mirror<\/a>).<\/li>\n
  4. Import MethFlowVM<\/sup>\u00a0to VirtualBox by double-clicking.<\/li>\n
  5. Optional: add a shared folder<\/a> (strongly recommended).<\/li>\n
  6. Run MethFlowVM<\/sup><\/li>\n<\/ol>\n

    The local database<\/h3>\n

    Set your\u00a0working\u00a0folder<\/strong><\/h4>\n

    At first startup, you will be asked which working folder you want to use. If you ignore this question, your home folder, \/home\/methflow<\/em>, will be used as working folder.<\/p>\n

    If you want to change the working folder, open a terminal and type the following command:<\/p>\n

    MethFlow_manager working_folder<\/strong><\/pre>\n
    Set your assembly collection<\/strong><\/h4>\n
    Tell MethFlow where the assembly collection is by typing:<\/p>\n
    MethFlow_manager assembly_collection Assemblies<\/strong><\/pre>\n
    This command\u00a0looks for\u00a0a folder named\u00a0Assemblies<\/em>\u00a0inside the working folder.<\/p>\n
    Set your\u00a0adapter collection<\/strong><\/h4>\n
    Tell MethFlow where the adapter collection is by typing:<\/p>\n
    MethFlow_manager adapter_collection Adapters<\/strong><\/pre>\n
    This command\u00a0looks for\u00a0a folder named\u00a0Adapters<\/em>\u00a0inside the working folder.<\/p>\n
    Set your root input folder<\/strong><\/h4>\n
    Tell MethFlow where to\u00a0look for\u00a0the input folders:<\/p>\n
    MethFlow_manager root_input_folder Inputs<\/strong><\/pre>\n
    This command\u00a0looks for\u00a0a folder named\u00a0Inputs<\/em>\u00a0inside the working folder.<\/p>\n
    Set your root output folder<\/strong><\/h4>\n
    Tell MethFlow where to kept the output folders:<\/p>\n
    MethFlow_manager root_output_folder Outputs<\/strong><\/pre>\n
    This command creates a folder named\u00a0Outputs<\/em> inside the working folder.<\/p>\n
    Get test datasets<\/strong><\/h3>\n
    Open a terminal and type the following command to get test datasets:<\/p>\n
    MethFlow_manager get_test_datasets<\/strong><\/pre>\n
    Test datasets are then downloaded and unpacked.<\/p>\n
    These test datasets contain:<\/p>\n