Reproduction pipeline for XXXXX.

For a general introduction to reproducible science as done here, please see
the link below:

  http://akhlaghi.org/reproducible-science.html



Running the pipeline
====================

To reproduce the results, please take these steps in order:

1. Make sure you have the dependencies (below).

2. Edit `reproduce/config/pipeline/DIRECTORIES.mk'.

   This file keeps the important top-level directories for this pipeline in
   your system. Open it with a text editor and give the necessary
   locations. The comments in this file (lines starting with a `#') should
   help in understanding the purpose of each directory.

   In short, if you don't have the input files on your system, this
   pipeline will download them in the specified directory. Also, the
   intermediate/build directory may be relatively large (~1GB), so please
   choose a build location with sufficient space.

3. Run the following command to reproduce everything on 8 threads. If your
   CPU has a different number of threads, change the number.

     $ make -j8



Output
======

The output of the pipeline is a PDF file, describing the published paper.



Dependencies
============

To reproduce the results you need the following programs. Except for
Gnuastro, the version of the other programs will not make a difference.

  Gnuastro Y.Y
  ------------

  Gnuastro is a large collection of programs for astronomical data analysis
  on the command-line. This is an intermediate version of Gnuastro (the
  tarball is not officially released on the Gnuastro webpage). However,
  this pipeline will ONLY work with this version of Gnuastro. For
  convenience, this tarball is available in the following link:

    https://zenodo.org/record/ZZZZZZ/files/gnuastro-Y.Y.tar.gz

  To uncompress, build and install the Gnuastro tarball, follow the
  instructions in the link below.

    https://www.gnu.org/software/gnuastro/manual/html_node/Quick-start.html

  If you successfully downloaded the tarball from the link above, please
  ignore the rest of this section on Gnuastro. If not, this version of
  Gnuastro is always present in Gnuastro's version controlled history and
  this reproduction pipeline contains the fix to implement to it.

  To build the above version of Gnuastro, please clone Gnuastro and
  checkout this version as shown in the following commands:

    $ git clone http://git.sv.gnu.org/r/gnuastro.git
    $ git checkout Y.Y

  Afterwords, you need to bootstrap Gnuastro as described in the following
  link.

    https://www.gnu.org/software/gnuastro/manual/html_node/Bootstrapping.html

  You are now ready to configure, build and install Gnuastro as described
  in the "Quick start" link above.



  AWK
  ---

  AWK is a program for working with text files. GNU AWK is the most common
  implementation and it is commonly already installed on most systems.



  flock
  -----

  This is a small program to manage file locks from the command-line. It is
  available in most GNU/Linux distributions.

  If you can't find it in your package manager or on some Mac OS systems,
  please put a copy of `reproduce/src/flock' file into your search path
  (this script needs Perl, so have that installed is well). To learn more
  about the search path and where to install this file, please see the link
  below. Before running this pipeline you should be able to run the `flock'
  command on your command-line.

    https://www.gnu.org/software/gnuastro/manual/html_node/Installation-directory.html



  Wget or cURL
  ------------

  These programs (`wget' or `curl' on the command-line) are used to
  download the input files if you don't already have them.



  LaTeX
  -----

  LaTeX is used to build the final PDF of this pipeline. Some important
  packages within LaTeX that this pipeline uses are: `biblatex' and
  `pgfplots'.