2. Installation

The Recipe System is distributed as part of DRAGONS. DRAGONS is available as a conda package. The installation instructions below will install all the necessary dependencies.

The use of the bash shell is required by Anaconda.

2.1. Install Anaconda

If you already have Anaconda installed, you can skip this step and go to the Install DRAGONS section below. If not, then your first step is to get and install Anaconda. You can download it at:

Choose the version of Python that suits your other Python needs. DRAGONS is compatible with Python 3.7. We recommend that you install the standard Python 3 version of Anaconda, the specific Python version can be adjusted later.

If you have downloaded the graphical installer, follow the graphical installer instructions. Install in your home directory. It should be the default.

If you have downloaded the command-line installer, type the following in a terminal, replacing the .sh file name to the name of the file you have downloaded. The /bin/bash -l line is not needed if you are already using bash. The command-line installer allows for more customization of the installation.

$ /bin/bash -l
$ chmod a+x Anaconda3-2019.03-MacOSX-x86_64.sh
$ ./Anaconda3-2019.03-MacOSX-x86_64.sh

($ indicates the terminal prompt.)


To prevent the Anaconda “base” environment from loading automatically, do:

$ conda config --set auto_activate_base false

2.2. Install DRAGONS

Anaconda requires the use of the bash shell. tcsh or csh will not work. If you are using (t)csh, your first step is:

$ /bin/bash -l

Make sure that ~/anaconda3/bin/activate is in your PATH by doing:

$ which activate

The Anaconda installer should have added conda configurations to the ~/.bash_profile for you. If activate is not found, try:

$ source ~/.bash_profile

If activate is still not found, you might have to add export PATH=~/anaconda3/bin:$PATH to your ~/.bash_profile using your favorite text editor, and run the source command above again.


Sometimes the Anaconda installer will install the software in ~/anaconda3 instead of simply ~/anaconda. Just check in your home directory which one of the tow possibilities was used.

The code Anaconda adds to the .bash_profile will automatically activate anaconda. To activate or deactivate Anaconda manually:

$ conda activate
$ conda deactivate

Now that Anaconda works, we add the needed astronomy software. Add the Astroconda channel and the Gemini channel. Those channels host the conda astronomy packages.

$ conda config --add channels http://ssb.stsci.edu/astroconda
$ conda config --add channels http://astroconda.gemini.edu/public

The next step is to create a virtual environment and install the DRAGONS software and its dependencies in it. The name of the environment can be anything you like. Here we use “dragons” as the name and we install Python 3.7.

$ conda create -n dragons python=3.7 dragons

Or, to include things like ds9

$ conda create -n dragons python=3.7 dragons stsci

Most users will probably want to install the extra astronomy tools that come with the stsci conda package.

To use this environment, activate it:

$ conda activate dragons

You will need to activate the environment whenever you start a new shell. If you are planning to use it all the time, you might want to add the command to your .bash_profile, after the “conda init” block.


As a side note, if you are going to use PyRAF regularly, for example to reduce Gemini data not yet supported in DRAGONS, you should be installing Python 2.7 as well in a different environment, along with the gemini, iraf-all and pyraf-all conda packages. Do not use PyRAF from the Python 3 environment; PyRAF is very slow under Python 3.

$ conda create -n geminiconda python=2.7 iraf-all pyraf-all stsci gemini

DRAGONS and the Recipe System do not need IRAF, PyRAF. Only DRAGONS v2 is compatible with Python 2.7. See the Gemini website for information on how to configure IRAF (http://www.gemini.edu/node/11823)

2.3. Configure DRAGONS

DRAGONS requires a configuration file located in ~/.geminidr/:

$ cd ~
$ mkdir .geminidr
$ cd .geminidr
$ touch rsys.cfg

Open rsys.cfg with your favority editor and add these lines:

standalone = True
database_dir = ~/.geminidr/

Then configure ds9 buffer configurations:

$ cd ~
$ cp $CONDA_PREFIX/lib/python3.7/site-packages/gempy/numdisplay/imtoolrc ~/.imtoolrc
$ vi .bash_profile   # or use your favorite editor

  Add this line to the .bash_profile:
    export IMTOOLRC=~/.imtoolrc

2.4. Test the installation

Start up the Python interpreter and import astrodata and the gemini_instruments packages:

$ python
>>> import astrodata
>>> import gemini_instruments

If the imports are successful, i.e. no errors show up, exit Python (Ctrl-D).

Now test that reduce runs. There may be some delay as package modules are compiled and loaded:

$ reduce --help

This will print the reduce help to the screen.

If you have Gemini FITS files available, you can test that the Recipe System is functioning as expected as follow (replace the file name with the name of your file):

$ reduce N20180106S0700.fits -r prepare

If all is well, you will see something like:

                    --- reduce, v3.0.0 ---
All submitted files appear valid
Found 'prepare' as a primitive.
RECIPE: prepare
PRIMITIVE: prepare
  PRIMITIVE: validateData
  PRIMITIVE: standardizeStructure
  PRIMITIVE: standardizeHeaders
     PRIMITIVE: standardizeObservatoryHeaders
     Updating keywords that are common to all Gemini data
     PRIMITIVE: standardizeInstrumentHeaders
     Updating keywords that are specific to NIRI
Wrote N20180106S0700_prepared.fits in output directory

reduce completed successfully.