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rdms:access:linux:irodsfs [2024/11/11 15:24] – Updated config files for newer irodsfs versions jelterdms:access:linux:irodsfs [2026/05/21 13:00] (current) – burcu
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 While you can access your RDMS collections by connecting to the RDMS remotely when using ''iCommands'', you can also create a space on your machine where you can access the RDMS directly as if it were part of your local directory hierarchy. This action of making a remote directory available on your local system is called "mounting" in technical terms. While you can access your RDMS collections by connecting to the RDMS remotely when using ''iCommands'', you can also create a space on your machine where you can access the RDMS directly as if it were part of your local directory hierarchy. This action of making a remote directory available on your local system is called "mounting" in technical terms.
  
-Linux users are able to mount iRODS collections and data objects (i.e. the iRODS version of directories and files) in their local directory hierarchy by using ''irodsfs'', a FUSE implementation of the iRODS client that you can download here: https://github.com/cyverse/irodsfs. +Linux users are able to mount iRODS collections and data objects (i.e., the iRODS version of directories and files) in their local directory hierarchy by using ''irodsfs'', a FUSE implementation of the iRODS client that you can download here: https://github.com/cyverse/irodsfs. 
  
-In this way, you can access data stored on an iRODS system, in our case on the RDMS, via the local directory hierarchy. This also allows you to use common Linux tools, e.g. ''rsync'', ''cp'', ''mkdir'' or ''vi'', to transfer, read, and/or organize the files present on the RDMS.+In this way, you can access data stored on an iRODS system, in our case on the RDMS, via the local directory hierarchy. This also allows you to use common Linux tools, e.g., ''rsync'', ''cp'', ''mkdir'' or ''vi'', to transfer, read, and/or organize the files present on the RDMS.
  
 The ''irodsfs'' package is pre-installed on the (virtual) Linux workplace and can be invoked by running the ''irodsfs'' command from the terminal. The ''irodsfs'' package is pre-installed on the (virtual) Linux workplace and can be invoked by running the ''irodsfs'' command from the terminal.
  
-For other Linux systems, the developer of ''irodsfs'' provides pre-built binaries which you can download from **Releases** on the official Github instance of the project (https://github.com/cyverse/irodsfs/releases).+For other Linux systems, the developer of ''irodsfs'' provides pre-built binaries which you can download from **Releases** on the official GitHub instance of the project (https://github.com/cyverse/irodsfs/releases).
  
  
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 To install and set up ''irodsfs'' on your personal Linux environment, follow steps 1-4. If you use the LWP instead, ''irodsfs'' is already preinstalled, and steps 1 and 2 can be skipped.  To install and set up ''irodsfs'' on your personal Linux environment, follow steps 1-4. If you use the LWP instead, ''irodsfs'' is already preinstalled, and steps 1 and 2 can be skipped. 
  
-1. Download the correct ''irodsfs'' version from Github (https://github.com/cyverse/irodsfs), either via browser or terminal. In this example, the download is performed using ''wget'' and the file is downloaded to your home directory.+1. Download the correct ''irodsfs'' version from GitHub (https://github.com/cyverse/irodsfs), either via browser or terminal. In this example, the download is performed using ''wget'' and the file is downloaded to your home directory.
 <code> <code>
  
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 **Notes:** **Notes:**
-  * Older version of ''irodfs'' used different termins in the config file, please be sure that you use the current ''irodsfs'' version.+  * Older version of ''irodfs'' used different terms in the config file, please be sure that you use the current ''irodsfs'' version.
   * Depending on your Linux distribution (e.g. CentOS), you might need to adjust ''/etc/ssl/certs/ca-certificates.crt'' to ''/etc/ssl/certs/ca-bundle.crt'' or equivalent.   * Depending on your Linux distribution (e.g. CentOS), you might need to adjust ''/etc/ssl/certs/ca-certificates.crt'' to ''/etc/ssl/certs/ca-bundle.crt'' or equivalent.
-  * Keep in mind that your UG mail addressed needs to be specified in lowercase!+  * Keep in mind that your UG mail address needs to be specified in lowercase!
  
 Another important aspect is that you take care to verify that the correct username is specified in the configuration file. To access the RDMS, you need to input your RUG email as your username. Another important aspect is that you take care to verify that the correct username is specified in the configuration file. To access the RDMS, you need to input your RUG email as your username.
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 ===== Mounting and unmounting iRODS collections with irodsfs ===== ===== Mounting and unmounting iRODS collections with irodsfs =====
  
-Now that the set-up of ''irodsfs'' is complete and working, you can mount your RDMS/iRODS collection to your local file system by running:+Now that the setup of ''irodsfs'' is complete and working, you can mount your RDMS/iRODS collection to your local file system by running:
  
 <code> <code>
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 You will be prompted for your password, and if no error messages are shown, you can now access your personal RDMS directory mounted at ''~/irods_mount/'' or wherever you chose to mount the RDMS location in the previous command. You will be prompted for your password, and if no error messages are shown, you can now access your personal RDMS directory mounted at ''~/irods_mount/'' or wherever you chose to mount the RDMS location in the previous command.
  
-If you are using the version of ''irodsfs'' that is preinstalled on the LWP or if you specified the location of the ''irodsfs'' binary in your ''$PATH'' environment variable, you do not need to provide the absolute path to ''irodsfs'' in your command. The syntax to mount the drive therefore becomes:+If you are using the version of ''irodsfs'' that is preinstalled on the LWP or if you specified the location of the ''irodsfs'' binary in your ''$PATH'' environment variable, you do not need to provide the absolute path to ''irodsfs'' in your command. The syntax to mount the drive, therefore, becomes:
  
 <code> <code>
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 </code> </code>
  
-Once you are done and wish to unmount the previously mounted collection, in this example ''~/irods_mount/'', you can use the following command:+Once you are done and wish to unmount the previously mounted collection, in this example, ''~/irods_mount/'', you can use the following command:
  
 <code> <code>
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 ===== Additional tips ===== ===== Additional tips =====
  
-You can also map multiple RDMS collections to your chosen mount point using ''irodsfs''. To do so you have to adjust the `path_mapping` variable in the ''config.yaml'' file that contains the ''irodsfs'' configuration.+You can also map multiple RDMS collections to your chosen mount point using ''irodsfs''. To do so, you have to adjust the `path_mapping` variable in the ''config.yaml'' file that contains the ''irodsfs'' configuration.
  
 The example below shows the configuration needed to mount your personal **RDMS Home Drive** at ''~/irods_mountpoint/RDMS_Home'', along with a **RDMS Team Drive** that you belong to at ''~/irods_mountpoint/RDMS_Team''. The example below shows the configuration needed to mount your personal **RDMS Home Drive** at ''~/irods_mountpoint/RDMS_Home'', along with a **RDMS Team Drive** that you belong to at ''~/irods_mountpoint/RDMS_Team''.
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 While it is possible to provide your password directly in the ''config.yaml'' file as shown above, we strongly advise against doing so for security reasons.  While it is possible to provide your password directly in the ''config.yaml'' file as shown above, we strongly advise against doing so for security reasons. 
  
-You can also install and use ''irodsfs'' on other environments besides your own personal Linux machine. For example you can follow the guide above to install ''irodsfs'' on a **Windows Subsystem for Linux (WSL)** instance. In the same way you can install and use ''irodsfs'' on the **Hábrók HPC cluster**. Just connect via ''ssh'' to the cluster and follow the manual above as if working on your local Linux machine.+You can also install and use ''irodsfs'' on other environments besides your own personal Linux machine. For example, you can follow the guide above to install ''irodsfs'' on a **Windows Subsystem for Linux (WSL)** instance. In the same way, you can install and use ''irodsfs'' on the **Hábrók HPC cluster**. Just connect via ''ssh'' to the cluster and follow the manual above as if working on your local Linux machine.