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Installation
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim
The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH
(e.g., $HOME/bin
) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically. For platforms other than Ubuntu, please find your way and report back if interested.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global
.
The process should finish with a message similar to this (here we only called ./install
thus installing in the code directory):
Installing 'st-explorer' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global' command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.