ISIS3 | Integrated Software for Imagers and Spectrometers

This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ through conda.
Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: Anaconda installer, Miniconda installer. If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment. This will start the Anaconda installer which will guide you through the installation process. If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86_64.pkg) will be downloaded. Double-click on the file to start the installation process. After the installation has finished, open up a bash prompt in your terminal window.
Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: Anaconda installer, Miniconda installer
If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment. chmod +x Anaconda3-5.3.0-Linux-x86_64.sh ./Anaconda3-5.3.0-Linux-x86_64.sh This will start the Anaconda installer which will guide you through the installation process.
If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86_64.pkg) will be downloaded. Double-click on the file to start the installation process.
After the installation has finished, open up a bash prompt in your terminal window.
Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands: #Create a new conda environment to install ISIS in conda create -n isis #Activate the environment conda activate isis #Add the following channels to the environment conda config --env --add channels conda-forge conda config --env --add channels usgs-astrogeology #Verify you have the correct channels: conda config --show channels #You should see: channels: - usgs-astrogeology - conda-forge - defaults #The order is important. If conda-forge is before usgs-astrogeology, you will need to run: conda config --env --add channels usgs-astrogeology
The environment is now ready to download ISIS and its dependencies: conda install -c usgs-astrogeology isis=7.0.0
Finally, setup the environment variables: ISIS requires several environment variables to be set in order to run correctly. The variables include: ISISROOT and ISISDATA. More information about the ISISDATA environment variable and the ISIS Data Area can be found here. The following steps are only valid for versions of ISIS after 4.2.0. For older versions of ISIS follow the instructions in this readme file. There are two methods to configure the environment variables for ISIS: Using conda env config vars preferred Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8. This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed. To determine if your version of conda is recent enough run: conda --version If the version number is less than 4.8, update conda to a newer version by running: conda update -n base conda The version number should now be greater than 4.8. To use the built in environment variable configuration feature, first activate the environment by first running: conda activate isis After activation, the environment variables can be set using the syntax: conda config vars set KEY=VALUE. To set all the environment variables ISIS requires, run the following command, updating the path to ISISDATA as needed: conda env config vars set ISISROOT=$CONDA_PREFIX ISISDATA=[path to data directory] To make these changes take effect, re-activate the isis environment by running: conda activate isis The environment variables are now set and ISIS is ready for use every time the isis environment is activated. Note This method will not enable tab completion for arguments in C-Shell. Using the provided isisVarInit.py script: To use the default values for: $ISISROOT and $ISISDATA, run the ISIS variable initialization script with default arguments: python $CONDA_PREFIX/scripts/isisVarInit.py Executing this script with no arguments will result in $ISISROOT=$CONDA_PREFIX and $ISISDATA=$CONDA_PREFIX/data. The user can specify different directories for $ISISDATA using the optional value: python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory] Now every time the isis environment is activated, $ISISROOT and $ISISDATA will be set to the values passed to isisVarInit.py. This does not happen retroactively, so re-activate the isis environment with one of the following commands: for Anaconda 3.4 and up - conda activate isis prior to Anaconda 3.4 - source activate isis
The ISIS production Dockerfile automates the conda installation process above. You can either build the Dockerfile yourself or use the usgsastro/isis image from DockerHub. Usually you'll want to mount an external directory containing the ISIS data. The data is not included in the Docker image. Then download the data into /my/data/dir to make it accessible inside your container.
Download the production Docker file
Build the Dockerfile
Run the Dockerfile