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 comments (lines starting with an `#') in the file that is opened by `./configure' and set the directories accordingly. $ ./configure 3. Run the following command 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