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.


  GNU Make
  --------

  This reproduction pipeline uses some features that may not be
  present in other implementations of Make.


  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.


  Tar and Gzip
  ------------

  Tar is used for packaging multiple files into one and Gzip is used
  for compression. They are both very common software in Unix-like
  operating systems, so they are probably already available on your
  system.


  GNU Coreutils
  -------------

  Very basic command-line programs (for example `cp' or `mkdir'). They
  may be implemented differently in non-GNU systems (for example Mac
  OS). But have not actually been tested in Mac OS. Alternatively,
  there are ways to install Coreutils on Mac OS (for example with
  Homebrew), please do a search to find solutions. Please get in touch
  with us if any errors occur due to such basic programs.


  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'.