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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
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