Reproduction pipeline for XXXXXXX

For a general introduction to reproducible science as implemented in this
pipeline, please see the link below:

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



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

1. Necessary dependencies:

   1.1: Basic software building tools like C compiler, Make, and other
        tools found on most Unix-like systems (GNU/Linux, BSD, Mac OS, and
        others). All necessary dependencies will be built from source by
        the `./configure' script (next step).

   1.2: Tarball of dependencies. If they are already present (in a
        directory given at configuration time), they will be
        used. Otherwise, *GNU Wget* will be used to download any necessary
        tarball. The necessary tarballs are also collected in the link
        below for easy download:

          https://gitlab.com/makhlaghi/reproducible-paper-dependencies

2. Configure the environment (top-level directories in particular) and
   build all the necessary software for use in the next step. It is
   recommended to modify the directories. Please read the description of
   each necessary input clearly and set the best value. Note that the
   configure scripts also downloads, builds and locally installs many
   programs (pipeline dependencies). So it may take a while to complete.

     $ ./configure

3. Run the following command (local build of Make) to reproduce all the
   analysis and build the final `paper.pdf' on *8* threads. If your CPU has
   a different number of threads, change the number.

     $ ./.local/bin/make -j8