Install#

We do not have the resources to provide installation support, thus we provide a server with the latest and older versions installed that users with access rights can use. However, the installation process is simple, and is described below (we hope that in enough detail) so that users can follow the steps and end up with a running version of the pipeline.

Note

In this tutorial we use Miniconda3 as but you can also do it with Anaconda by visiting https://www.anaconda.com/download/ for downloading the Anaconda installer for either operating system.

Ubuntu#

This installation process has been tested in a live version (previously known as Live CD) of Ubuntu 18.04.

  1. Install make and gcc

sudo apt install gcc make

  1. Download Miniconda

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

Mac OS#

This installation was tested on MacOS High Sierra.

  1. Install Xcode command Line Tools. You can do it from the App Store or from command line.

xcode-select --install

  1. Download Anaconda or Miniconda

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh --output miniconda.sh

If you have a different processor like intel, you can search miniconda installer url for your system.

Common Steps#

Warning

This installation instructions work with BASH only.

  1. Install Miniconda

bash miniconda.sh

Answer the questions and reopen the terminal at the end.

  1. Configure conda to use the Astroconda Channel

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

  1. Get the latest release of the Goodman Spectroscopic Pipeline from github. There is a .zip and .tar.gz files, the following steps will continue with the latter.

    Make sure there is a green tag that says Latest release. For instance, for the version v1.1.2 the file is called.

    goodman_pipeline-1.2.1.tar.gz

  2. Extract the file (you can’t copy and paste this line)

tar -xvf goodman_pipeline-<latest tag>.tar.gz

where <latest tag> is the version number of the latest release.

  1. Move into the directory containing the package.

cd goodman_pipeline-<latest tag>

If you do ls you should find some interesting files on it such as: setup.py and environment.yml and install_dcr.sh.

  1. Create the virtual environment. The environment.yml file contains a preset definition of a virtual environment that Anaconda will understand, also ensures that the Goodman Spectroscopic Pipeline will work. Even the name of the virtual environment is set there.

conda env create -f environment.yml

This will create a virtual environment called goodman_pipeline. To activate it

source activate goodman_pipeline

  1. Install DCR. This script requires a virtual environment activated.

sh install_dcr.sh

To test if it worked you can do:

dcr

You should get something like this:

(goodman_pipeline) [user@servername goodman_pipeline]$ dcr

      This is a modified version of DCR! for the Goodman Spectroscopic Pipeline
      Please visit the author's site to get the original version:
      Modification Version: 0.0.1

      http://users.camk.edu.pl/pych/DCR/


      USAGE:  dcr  input_file  cleaned_file  cosmicrays_file

File 'dcr.par' must be present in the working directory.
    ~~~~~~

  1. Run tests.

python setup.py test

  1. Install the pipeline

python setup.py install

Using pip#

The Goodman Spectroscopic Pipeline Can also be installed using pip, but it does not install dcr, so if you are updating your goodman pipeline only you can use:

pip install goodman-pipeline

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