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.
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.
This installation process has been tested in a live version (previously known as Live CD) of Ubuntu 18.04.
sudo apt install gcc make
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
This installation was tested on MacOS High Sierra.
Install Xcode command Line Tools. You can do it from the App Store or from command line.
Download Anaconda or Miniconda
curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh --output miniconda.sh
This installation instructions work with BASH only.
Answer the questions and reopen the terminal at the end.
Configure conda to use the Astroconda Channel
conda config --add channels http://ssb.stsci.edu/astroconda
Get the latest release of the Goodman Spectroscopic Pipeline from github. There is a
.tar.gzfiles, the following steps will continue with the latter.
Make sure there is a green tag that says Latest release. For instance, for the version
v1.1.2the file is called.
Extract the file (you can’t copy and paste this line)
tar -xvf goodman_pipeline-<latest tag>.tar.gz
<latest tag>is the version number of the latest release.
Move into the directory containing the package.
cd goodman_pipeline-<latest tag>
If you do
lsyou should find some interesting files on it such as:
Create the virtual environment. The
environment.ymlfile 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
DCR. This script requires a virtual environment activated.
To test if it worked you can do:
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. ~~~~~~
python setup.py test
Install the pipeline
python setup.py install
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