![]() Once you have Fiji up and running, you will probably want to open some images. However we have not yet investigated how to run the Fiji UI with Kitematic. It makes it very easy to download and run new images. Kitematic is a UI-oriented way to start Docker containers on Macs. Where the IP address was what we found earlier with ifconfig.Ĭongratulations! You should now be running Fiji in a Docker image. In the second terminal, you can now use Docker to launch a Fiji GUI. Socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\" You will want two X11 terminals open here ( Application > Terminal to open a new X11 terminal). withįrom this same terminal, open XQuartz with: Now, in the same terminal you started boot2docker, you should have set up the environment variables e.g. Since you are using OSX it is assumed you are using boot2docker. Inet 192.168.15.2 netmask 0xffffffff broadcast 192.168.0.0Īnd take note of the ip address on the last line ( 192.168.15.2 in this case). Which will print output that should end with something like: Then, from a terminal, use Homebrew to install socat and XQuartz via:Īnd ensure it is not empty (it should print something like /private/tmp/5TvcMIf/:0). To get a GUI application running on OSX, we can adapt the techniques discussed in this docker issue to run an X11 session, and share it with Docker.įirst, you will need to install the following: Which should pop up a window with Fiji running. # Modify this tag if a different java version is desiredĮcho "developer:x:$:" > /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). ![]() 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. Thus, to remove this error open your command terminal and install it.Docker provides a platform for distribution of application state. The error appears because the Kitematic is unable to find the default set Xterm command-line terminal application on your system. “null does not exist please set the correct path” Kitematic Error solution. It appears when after installing Kitematic you either click on Docker CLI or EXEC option given for each container. See our tutorial- How to install Kitematic docker manager on RedHat-based OS such as CentOS and others…Ĭoming to the error that is “ The null does not exist please set the correct path“. But if you want then can install the Kitematic on RHEL based Linux such as CemtOS, Rocky, AlmaLinux, and others. It is available for Windows, macOS, and Ubuntu Linux operating systems. Kitematic is an open-source project that makes it easier to get started with Docker by offering a graphical interface with which containers from the Docker Hub registry can be selected and used comparatively easily. If you are using Kitematic to manage Docker machines and while accessing Containers’ CLI – you get an error “The null does not exist please set the correct path” then here is the solution for that. ![]()
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