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search.json

@@ -5343,7 +5343,7 @@
     "href": "tools/yoda/yoda_using_icommands.html#installing-irods-icommands",
     "title": "Using iCommands",
     "section": "Installing iRODS iCommands",
-    "text": "Installing iRODS iCommands\nNative iRODS iCommands packages are available for CentOS and Ubuntu.\nWindows 10/11 users can run the iCommands in the Windows Subsystem for Linux. There is no officially supported iCommands installation for Mac OSX, you could install the iCommands inside a Linux VM.\n\n\n\n\n\n\nTip\n\n\n\ngocommands is an alternative command-line client you could try if your OS does not support iCommands. The Handbook explains how to install and use it.\n\n\n\nInstalling iCommands on CentOS\nThe following should work to install the iCommands on CentOS 8.\n\nFirst add the package source:\n\nsudo yum -y install wget epel-release yum-plugin-versionlock\nsudo rpm --import https://packages.irods.org/irods-signing-key.asc\nwget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo\n\nNote that the latest iRODS version is 5, this client is not compatible with the Yoda iRODS version.You can list the available versions with:\n\nsudo yum --showduplicates list irods-icommands\n\nInstall the latest available 4.x.x version:\n\nsudo yum -y install irods-runtime-4.3.0 irods-icommands-4.3.0\nsudo yum versionlock irods-runtime irods-icommands\n\nUpgrading from an earlier version\nIf you have put packages irods-runtime and irods-icommands on hold, you should first release the hold. Otherwise, the instruction is the same as above.\n# Show applied locks, if any\nyum versionlock list\nyum versionlock delete irods-runtime irods-icommands\n\n\n\nInstalling iCommands on Ubuntu\nThe following should work to install the iCommands on Ubuntu 22 or 24.\n\nFirst add the iRODS package source.\n\nwget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -\necho \"deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main\" | sudo tee /etc/apt/sources.list.d/renci-irods.list\nsudo apt update\n\nNote that the latest iRODS version is 5, this client is not compatible with the Yoda iRODS version. You can check which versions are available with:\n\nsudo apt show irods-icommands -a\n\nTake the latest 4.x version, at the time of writing:\n\nsudo apt -y install irods-runtime=4.3.4-0~noble irods-icommands=4.3.4-0~noble\n\nMake sure to hold the package to prevent inadvertently updating to version 5:\n\nsudo apt-mark hold irods-runtime irods-icommands\n\nUpgrading from an earlier version\nIf you have put packages irods-runtime and irods-icommands on hold, you should first release the hold. Otherwise, the instruction is the same as above.\n# Show applied holds, if any\napt-mark showhold\napt-mark unhold irods-runtime irods-icommands",
+    "text": "Installing iRODS iCommands\nNative iRODS iCommands packages are available for CentOS and Ubuntu.\nWindows 10/11 users can run the iCommands in the Windows Subsystem for Linux. There is no officially supported iCommands installation for Mac OSX, you could install the iCommands inside a Linux VM.\n\n\n\n\n\n\nTip\n\n\n\ngocommands is an alternative command-line client you could try if your OS does not support iCommands. The Handbook explains how to install and use it.\n\n\n\nInstalling iCommands on CentOS\nThe following should work to install the iCommands on supported CentOS or Red Hat versions.\n\nFirst add the package source:\n\nsudo yum -y install wget epel-release yum-plugin-versionlock\nsudo rpm --import https://packages.irods.org/irods-signing-key.asc\nwget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo\nNote that Yoda 2.1 uses iRODS server version 5.0.2, any version 5 client should work. You can list the available versions with:\nsudo yum --showduplicates list irods-icommands\n\nInstall the latest available version:\n\nsudo yum -y install irods-runtime irods-icommands\nMake sure to lock the package to prevent inadvertently updating to an unsupported version:\nsudo yum versionlock irods-runtime irods-icommands\n\nUpgrading from an earlier version\nIf you have put packages irods-runtime and irods-icommands on hold, you should first release the hold. Otherwise, the instruction is the same as above.\n# Show applied locks, if any\nyum versionlock list\nyum versionlock delete irods-runtime irods-icommands\n\n\n\nInstalling iCommands on Ubuntu\nThe following should work to install the iCommands on Ubuntu 22 or 24.\n\nFirst add the iRODS package source and key.\n\nsudo mkdir -p /etc/apt/keyrings\nwget -qO - https://packages.irods.org/irods-signing-key.asc | \\\n    sudo gpg \\\n        --no-options \\\n        --no-default-keyring \\\n        --no-auto-check-trustdb \\\n        --homedir /dev/null \\\n        --no-keyring \\\n        --import-options import-export \\\n        --output /etc/apt/keyrings/renci-irods-archive-keyring.pgp \\\n        --import\necho \"deb [signed-by=/etc/apt/keyrings/renci-irods-archive-keyring.pgp arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main\" | \\\n     sudo tee /etc/apt/sources.list.d/renci-irods.list\nsudo apt update\nNote that Yoda 2.1 uses iRODS server version 5.0.2, any version 5 client should work. You can list the available versions with:\nsudo apt show irods-icommands -a\n\nInstall the latest version:\n\nsudo apt -y install irods-runtime irods-icommands\nMake sure to hold the package to prevent inadvertently updating to an unsupported version:\nsudo apt-mark hold irods-runtime irods-icommands\n\nUpgrading from an earlier version\nIf you have put packages irods-runtime and irods-icommands on hold, you should first release the hold. Otherwise, the instruction is the same as above.\n# Show applied holds, if any\napt-mark showhold\napt-mark unhold irods-runtime irods-icommands",
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     "href": "tools/yoda/yoda_using_icommands.html#environment-file",
     "title": "Using iCommands",
     "section": "Environment file",
-    "text": "Environment file\nThe iCommands need to be configured to connect to the right Yoda environment.\nPlease copy and paste this configuration into your ~/.irods/irods_environment.json configuration file.\nYou will need to change the example user name to your Yoda user name.\n{\n    \"irods_host\": \"portal.yoda.vu.nl\",\n    \"irods_port\": 1247,\n    \"irods_home\": \"/vu/home\",\n    \"irods_user_name\": \"xxx@vu.nl\",\n    \"irods_zone_name\": \"vu\",\n    \"irods_default_resource\": \"irodsResc\",\n    \"irods_authentication_scheme\": \"pam_password\",\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    \"irods_client_server_policy\": \"CS_NEG_REQUIRE\"\n}\n\n\n\n\n\n\nImportant\n\n\n\nPlease note that irods_authentication_scheme has changed from pam to pam_password in Yoda 2.0.\n\n\nYou can also copy the contents from the “Data Transfer” page on the Yoda Portal:",
+    "text": "Environment file\nThe iCommands need to be configured to connect to the right Yoda environment.\nPlease copy and paste this configuration into your ~/.irods/irods_environment.json configuration file.\nYou will need to change the example irods_user_name to your Yoda user name.\n{\n    \"irods_host\": \"portal.yoda.vu.nl\",\n    \"irods_port\": 1247,\n    \"irods_home\": \"/vu/home\",\n    \"irods_user_name\": \"xxx@vu.nl\",\n    \"irods_zone_name\": \"vu\",\n    \"irods_default_resource\": \"irodsResc\",\n    \"irods_authentication_scheme\": \"pam_password\",\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    \"irods_client_server_policy\": \"CS_NEG_REQUIRE\"\n}\n\n\n\n\n\n\nImportant\n\n\n\nPlease note that irods_authentication_scheme has changed from pam to pam_password in Yoda 2.0.\n\n\nYou can also copy the contents from the “Data Transfer” page on the Yoda Portal:",
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@@ -5369,7 +5369,7 @@
     "href": "tools/yoda/yoda_using_icommands.html#getting-started-with-icommands",
     "title": "Using iCommands",
     "section": "Getting started with iCommands",
-    "text": "Getting started with iCommands\nAfter installing and configuring the iCommands, you should be able to log in on the Yoda environment using the iinit command. Enter a Yoda Data Access Password when prompted.\nThese are the basic commands for navigation and data transfer:\n\nipwd – Show current iRODS directory\nils – List contents of a directory\nicd – Change directory\niput – Upload files to Yoda\niget – Download files from Yoda\nirsync – Synchronize local and remote directories\n\nYour Yoda project folders are located under /vu/home.\n\n\n\n\n\n\nTip\n\n\n\nBy default an iRODS session will time-out after an hour and you will need to login again. You can extend the session by starting it with the --ttl <hours> option, e.g. iinit --ttl 8 will keep the session alive for 8 hours.\n\n\nYou can find a quick introduction of the iCommands on the SURF wiki or you can check out this training manual.\nYou can find a full list of available commands in the iRODS Docs.",
+    "text": "Getting started with iCommands\nAfter installing and configuring the iCommands, you should be able to log in on the Yoda environment using the iinit command. Enter a Yoda Data Access Password when prompted.\nThese are the basic commands for navigation and data transfer:\n\nipwd – Show current iRODS directory\nils – List contents of a directory\nicd – Change directory\niput – Upload files to Yoda\niget – Download files from Yoda\nirsync – Synchronise local and remote directories\n\nYour Yoda project folders are located under /vu/home.\n\n\n\n\n\n\nTip\n\n\n\nBy default an iRODS session will time-out after an hour and you will need to login again. You can extend the session by starting it with the --ttl <hours> option, e.g. iinit --ttl 8 will keep the session alive for 8 hours.\n\n\nYou can find a quick introduction of the iCommands on the SURF wiki or you can check out this training manual.\nYou can find a full list of available commands in the iRODS Docs.",
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