First commit to the reproduction pipeline template

Let's start working on this pipeline independently with this first
commit. It is based on my previous experiences, but I had never made a
skeleton of a pipeline before, it was always within a working analysis.

But now that the pipeline has a separate repository for its self, we will
be able to work on it and use it as a base for future work and modify it to
make it even better. Hopefully in time (and with the help of others), it
will grow and become much more robust and useful.

1 files changed, 153 insertions, 0 deletions

diff --git a/README b/README
new file mode 100644
index 0000000..95b53b6
--- /dev/null
+++ b/README
@@ -0,0 +1,153 @@
+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'.