Frequently Asked Questions

When should I use iBridges instead of python-irodsclient/iCommands?

The python-irodsclient and the iCommands are much more powerful and expressive than iBridges. If you are already intimately familiar with either of them, you probably don’t need iBridges, since it doesn’t add any functionality that isn’t already there.

The target audience of iBridges is different: it tries to help researchers/users that are not expert iRODS users. The learning curve of using iBridges is much easier than either of the two alternatives. Additionally, its simplicity and default checks makes it less likely you will end up with bad data.

An advantage compared to the iCommands is that iBridges also works on Mac OS and Windows.

I found a bug or have a feature request, where do I go?

Our development is done on GitHub Look under the Issues section whether the bug or feature request has already been reported. If not, we heartily welcome creating a new issue. We try to get back to you as soon as possible, at least within a few days.

I want to contribute to iBridges, where do I go?

Our development is done on GitHub We are welcoming contributions by pull requests. You can also ask for new features/ideas in our issue tracker.

I have installed iBridges and now get “ibridges: command not found”

This can happen for a variety for reasons, but the most common reason is that your PATH is not setup correctly on your system. Often pip will complain about this when you install ibridges. To solve this, you must first find out where pip installs the ibridges executable. Usually this will be something like /home/your_username/.local/bin, but this is dependent on your system. Then we must add this to the path on the command line: export PATH=”${PATH}:/home/your_username/.local/bin” (change the path according to your system). This should allow your shell to find the ibridges command. You would have to type the previous command every time you start a new shell, which can be inconvenient. To fix this permanently, add the command to your .bashrc or .zshrc file in your home directory at the end of the file (depending on your shell, type echo ${SHELL} to find out).

Help, I’m getting a “NetworkError” while trying to transfer (large) files

This error is most likely to happen if you try to transfer a large file. The default timeout for iBridges is 25000 seconds, which translates to roughly 7 hours. This should not cause issues during the actual transfer. However, if the calculation of the checksum takes more than 7 hours (if the iRODS server is busy for example, or the file is many terabytes), then you will get a network error. The checksum itself should still be created. You can increase the timeout in your irods_environment.json file by adding a new entry with "connection_timeout": 99999999999,.