Inet 192.168.15.2 netmask 0xffffffff broadcast 192.168.0.0Īnd take note of the ip address on the last line ( 192.168.15.2 in this case). Which will print output that should end with something like: Then, from a terminal, use Homebrew to install socat and XQuartz via:Īnd ensure it is not empty (it should print something like /private/tmp/5TvcMIf/:0). To get a GUI application running on OSX, we can adapt the techniques discussed in this docker issue to run an X11 session, and share it with Docker.įirst, you will need to install the following: Which should pop up a window with Fiji running. # Modify this tag if a different java version is desiredĮcho "developer:x:$:" > /etc/group & \Įcho "developer ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/developer & \ We can adapt this blog post on running GUI applications with Docker to share the X11 port. Please report issues and contribute suggestions if you have ideas for improving interoperability between Fiji's UI and Docker. Note that this is highly experimental right now, and the steps to get Fiji running can be fairly involved. However, it is not impossible on other architectures. Docker has tight Linux integration, so it is much easier to share displays with a Docker image if you are using a Linux host. This is, unfortunately, currently quite platform-specific. to install additional plugins or utility software, you can start the command prompt via: If you want to manually explore the Fiji Docker image, e.g. To start a headless ImageJ invocation from Docker, use:ĭocker run -it -rm fiji/fiji fiji-linu圆4 -headless Running ImageJ headlessly in Docker is not much different than normal headless operation - see the headless guide for general information.
The following sections cover headless and graphical uses. So if you just tried one of the above commands, you likely got an error: Important - without some extra setup, there is no display used by Docker. For example, if you wanted to run with Oracle's Java 6, you would use:ĭocker run -it -rm fiji/fiji:fiji-oracle-jdk6 Several tags are provided to run Fiji with different Java versions. Will call the default Fiji image, attempting to open the ImageJ UI with Java 7. These images call the Fiji executable by default. The base Fiji images are provided on Docker Hub. You will need to install Docker for your system. These images can then be reused by remote users and scientists worldwide, with no dependency concerns (beyond Docker itself).
#BREW INSTALL SOCAT UPDATE#
This facilitates the highest level of scientific reproducibility - as a Docker image can bundle operating system, Java version, update site and plugin state, and even sample data. Docker provides a platform for distribution of application state.
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