configuration.md 2.29 KB
 Jeff Thiessen committed Dec 06, 2018 1 2 3 4 5 6 7 8 ## Configuration To use the IRIDA uploader, you will need to create a client in IRIDA for the uploader. Please refer to the ["Configure the Uploader" section on the IRIDA tutorials](https://irida.corefacility.ca/documentation/user/tutorials/uploader-tool/) for more information. ###File Location  Jeff Thiessen committed Dec 11, 2018 9 You can create the config file yourself, or simply run the uploader for the first time to create a new config file with empty/default values.  Jeff Thiessen committed Dec 06, 2018 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26  You can find this file: Linux: ~/.config/irida-uploader/config.conf Windows: C:\Users\\AppData\Local\irida-uploader\config.conf ###Options The config file has the following fields: * client_id : The id from the IRIDA client you created * client_secret : The secret from the IRIDA client you created * username : The user that will be accessing projects/samples, this user needs the Sequencer or Administrator role. * password : Corresponding password for above user. * base_url : The server URL is the location that the uploader should upload data to. If you navigate to your instance of IRIDA in your web browser, the URL (after you’ve logged in) will often look like: https://irida.corefacility.ca/irida/. The URL you should enter into the Server URL field is that URL, with api/ at the end. So in the case of https://irida.corefacility.ca/irida/, you should enter the URL https://irida.corefacility.ca/irida/api/ * parser : Pick the parser that matches the file structure of your sequence files. We currently support [miseq](parsers/miseq.md) and [directory](parsers/directory.md).  Jeff Thiessen committed Dec 13, 2018 27 28 29 30 31 32 33 34 35 36 37  ###Example  [Settings] client_id = uploader client_secret = ZK1z6H165y4IZF2ckqNQES315OyKQU8CsrpHNdQr16 username = admin password = password1 base_url = http://localhost:8080/irida-latest/api/ parser = miseq  Jeff Thiessen committed Dec 17, 2018 38   Jeff Thiessen committed Jan 24, 2019 39 This can also be found in the file example_config.conf  Jeff Thiessen committed Dec 17, 2018 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59  ## Specify other config file Alternatively, you can pass a config file to the command line uploader as an optional argument. Use -c or --config and specify the path to your config file. Example:  # Linux \$ ./irida-uploader.sh --config /path/to/config.conf /path/to/the/sequencing/run/ # Windows C:\Users\username> iridauploader --config \path\to\config.conf \path\to\my\samples\  ### Linux: Use the the irida-uploader.sh script included with the source code to upload.