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| "href": "docs/manuals/ibridges.html", | ||
| "title": "Using iBridges on SURF Research Cloud", | ||
| "section": "", | ||
| "text": "The instructions below describe the how to setup iBridges to transfer data between SURF Research Cloud and Yoda or any other iRODS instance. It is possible to use iBridges in three different ways:\n\nas a python package\nvia the command line interface (CLI)\nvia the graphical user interface (GUI)\n\nUsing any of the three methods you can safely and easily transfer large amounts of data between Yoda and your Research cloud workspace.\nThe python package and the command line interface are available (or can be made available) on all workspaces while the graphical user interface will only work on ‘Desktop’ workspaces, i.e. workspaces where you will have a Windows or Linux (e.g. Ubuntu) Desktop.\n\n\n\nibridges\n\n\n\nPrerequisites\nAccess to Yoda or another iRODS instance which hosts your data.\niBridges needs to be installed on your workspace. Many SURF ResearchCloud workspaces developed by Utrecht University (such as Python and R workbenches) have iBridges preinstalled.\n\nIf you are working on a Desktop workspace, you can check by logging in to your workspace, clicking ‘applications’ in the top left corner, and clicking ‘Development’.\nOn non-desktop workspaces check if iBridges is installed by typing: ibridges in the terminal. If iBridges is installed, this should show you the program’s help menu. On Jupyter or Rstudio workspaces, you need to open a terminal first: In Jupyter, click the + button in the file browser and select the terminal in the new Launcher tab (find a short video here). In Rstudio, In the bottom left panel, click the ‘terminal’ tab.\n\n\n\nConfigure iBridges\nTo connect to a Yoda or any other iRODS instance you will need a so-called irods_environment.json which needs to be stored in a specific location. You can create this file by hand or use the iBridges GUI or CLI to create it for you.\n\nConfiguration through the GUI\n\nOpen the GUI\n\nWindows: Go to the Main Menu and search for or click on the tile ibridges\nLinux: Go to Applications –> Development –> iBridges\n\nFrom the main menu click ‘Configure’ –> Add Configuration. Click on the template you want to use, fill in your user name and save the file as irods_environment.json in the suggested .irods folder.\n\nIf there are no templates in the drop-down menu of the configuration window, you will need to install the plugin. To this end you will need python and git and execute in power shell, git bash or Anaconda terminal:\npip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git\n\n\nConfiguration through the CLI\nIf you want to connect to a server hosted by Utrecht University please check whether this information is already present for ibridges.\nibridges setup --list\nFrom that list simply choose the server you want to connect to with ibridges setup uu-<server> and follow the instructions. In case you get the message No server information was found. please install:\npip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git\n\n\nWhat shall I do if iBridges is not on my workspace?\nIf your workspace has python installed, you can install the packages using the command line (or aka terminal):\n\nGUI: pip install ibridgesgui\nCLI/API: pip install ibridges\n\nTo start the GUI application you would then need to open a terminal and type in ibridges-gui. (Note: this will only work on Desktop workspaces).\nPlease contact us if you need help with installing iBridges or if you want to have iBridges preinstalled on your workspace.\n\n\nHow to connect to a Yoda or iRODS instance not provided by Yoda?\nIn this case you will have to create your irods_environment.json by hand:\nIn order to know with what server iBridges should connect, a so-called iRODS environment file must be present in your home directory.\nYou may need help from your datamanager or contact Yoda support to obtain the information needed for the config file.\nGo to your home directory and create a hidden directory called ‘.irods’:\ncd ~\nmkdir .irods\ncd .irods\nIn this directory, create a file named irods_environment.json.\ntouch irods_environment.json\nEdit the file using a text editor such as nano or vim:\nnano irods_environment.json\nGo to the yoda website, scroll to Step 2. Configuring iCommands and copy and paste the text belonging to your institution in the file (similar to the file below) and change the email address next to irods_user_nameto your yoda user name (typically your uu email address).\n{ \n\"irods_host\": \"science.data.uu.nl\", \n\"irods_port\": 1247, \"irods_home\": \"/nluu6p/home\", \n\"irods_user_name\": \"[email protected]\", \n\"irods_zone_name\": \"nluu6p\", \n\"irods_authentication_scheme\": \"pam\", \n\"irods_encryption_algorithm\": \"AES-256-CBC\", \n\"irods_encryption_key_size\": 32, \n\"irods_encryption_num_hash_rounds\": 16, \n\"irods_encryption_salt_size\": 8, \n\"irods_client_server_negotiation\": \"request_server_negotiation\"\n}\nFor a more extensive tutorial, see\n\nSetup by GUI\nSetup\n\n\n\n\nUsing iBridges\nTo use iBridges on Yoda hosted by Utrecht University you will need a data access password.\n\nGraphical user interface\nOnce you have an irods_environment.json, click on Connect –> Connect to iRODS, choose your irods_environment.json and provide your data access password\nIn the iBridges GUI documentation\n\n\nCommand line interface\nSimply try ibridges --help or ibridges <command> --help to get examples and help for the usage.\nFor instructions on how to use the ibridges command please see the iBridges documentation.\n\n\nUsing the python package\nWe offer tutorials in form of Jupyter notebooks to show you the capabilities of the ibridges python package.\nFor more information please see the iBridges documentation" | ||
| "text": "The instructions below describe the how to setup iBridges to transfer data between SURF Research Cloud and Yoda or any other iRODS instance. It is possible to use iBridges in three different ways:\n\nas a python package\nvia the command line interface (CLI)\nvia the graphical user interface (GUI)\n\nUsing any of the three methods you can safely and easily transfer large amounts of data between Yoda and your Research cloud workspace.\nThe python package and the command line interface are available (or can be made available) on all workspaces while the graphical user interface will only work on ‘Desktop’ workspaces, i.e. workspaces where you will have a Windows or Linux (e.g. Ubuntu) Desktop.\n\n\n\nibridges\n\n\n\nPrerequisites\nAccess to Yoda or another iRODS instance which hosts your data.\niBridges needs to be installed on your workspace. Many SURF ResearchCloud workspaces developed by Utrecht University (such as Python and R workbenches) have iBridges preinstalled.\n\nIf you are working on a Desktop workspace, you can check by logging in to your workspace, clicking ‘applications’ in the top left corner, and clicking ‘Development’.\nOn non-desktop workspaces check if iBridges is installed by typing: ibridges in the terminal. If iBridges is installed, this should show you the program’s help menu. On Jupyter or Rstudio workspaces, you need to open a terminal first: In Jupyter, click the + button in the file browser and select the terminal in the new Launcher tab (find a short video here). In Rstudio, In the bottom left panel, click the ‘terminal’ tab.\n\n\n\nConfigure iBridges\nTo connect to a Yoda or any other iRODS instance you will need a so-called irods_environment.json which needs to be stored in a specific location. You can create this file by hand or use the iBridges GUI or CLI to create it for you.\n\nConfiguration through the GUI\n\nOpen the GUI\n\nWindows: Go to the Main Menu and search for or click on the tile ibridges\nLinux: Go to Applications –> Development –> iBridges\n\nFrom the main menu click ‘Configure’ –> Add Configuration. Click on the template you want to use, fill in your user name and save the file as irods_environment.json in the suggested .irods folder.\n\nIf there are no templates in the drop-down menu of the configuration window, you will need to install the plugin. To this end you will need python and git and execute in power shell, git bash or Anaconda terminal:\npip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git\n\n\nConfiguration through the CLI\nIf you want to connect to a server hosted by Utrecht University please check whether this information is already present for ibridges.\nibridges setup --list\nFrom that list simply choose the server you want to connect to with ibridges setup uu-<server> and follow the instructions. In case you get the message No server information was found. please install:\npip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git\n\n\nWhat shall I do if iBridges is not on my workspace?\nIf your workspace has python installed, you can install the packages using the command line (or aka terminal):\n\nGUI: pip install ibridgesgui\nCLI/API: pip install ibridges\n\nTo start the GUI application you would then need to open a terminal and type in ibridges-gui. (Note: this will only work on Desktop workspaces).\nPlease contact us if you need help with installing iBridges or if you want to have iBridges preinstalled on your workspace.\n\n\nHow to connect to a Yoda or iRODS instance not provided by Yoda?\nIn this case you will have to create your irods_environment.json by hand:\nIn order to know with what server iBridges should connect, a so-called iRODS environment file must be present in your home directory.\nYou may need help from your datamanager or contact Yoda support to obtain the information needed for the config file.\nGo to your home directory and create a hidden directory called ‘.irods’:\ncd ~\nmkdir .irods\ncd .irods\nIn this directory, create a file named irods_environment.json.\ntouch irods_environment.json\nEdit the file using a text editor such as nano or vim:\nnano irods_environment.json\nGo to the yoda website, scroll to Step 2. Configuring iCommands and copy and paste the text belonging to your institution in the file (similar to the file below) and change the email address next to irods_user_nameto your yoda user name (typically your uu email address).\n{ \n\"irods_host\": \"science.data.uu.nl\", \n\"irods_port\": 1247, \"irods_home\": \"/nluu6p/home\", \n\"irods_user_name\": \"[email protected]\", \n\"irods_zone_name\": \"nluu6p\", \n\"irods_authentication_scheme\": \"pam\", \n\"irods_encryption_algorithm\": \"AES-256-CBC\", \n\"irods_encryption_key_size\": 32, \n\"irods_encryption_num_hash_rounds\": 16, \n\"irods_encryption_salt_size\": 8, \n\"irods_client_server_negotiation\": \"request_server_negotiation\"\n}\nFor a more extensive tutorial, see\n\nSetup by GUI\nSetup\n\n\n\n\nUsing iBridges\nTo use iBridges on Yoda hosted by Utrecht University you will need a data access password.\n\nGraphical user interface\nOnce you have an irods_environment.json, click on Connect –> Connect to iRODS, choose your irods_environment.json and provide your data access password.\nMore elaborate instructions can be found in the iBridges GUI documentation.\n\n\nCommand line interface\nSimply try ibridges --help or ibridges <command> --help to get examples and help for the usage.\nFor instructions on how to use the ibridges command please see the iBridges documentation.\n\n\nUsing the python package\nWe offer tutorials in form of Jupyter notebooks to show you the capabilities of the ibridges python package.\nFor more information please see the iBridges documentation" | ||
| }, | ||
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| "objectID": "docs/manuals/rclone-researchcloud.html", | ||
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