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@@ -1,76 +0,0 @@ -Reproduction pipeline for paper XXXXXXX -======================================= - -This is the reproduction pipeline for the paper titled "**XXXXXX**", by -XXXXXXXX et al. (**IN PREPARATION**). - -A *reproduction pipeline* contains the full instructions to configure and -build the necessary software packages used in the analysis, and uses them -*exactly* reproduce what we have published. All the scripts/instructions -are in a human *and* computer readable format (scripts and Makefiles). - -The only dependency for the pipeline is **Wget**, and a minimal Unix-based -building environment including a C compiler (already available on your -system if you have ever installed a software from source). Note that **Git -is not mandatory**: if you don't have Git to run the first command below, -go to the URL given in the command on your browser, and download them -manually (there is a button to download a compressed tarball of the -project). - -```shell -$ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -$ ./configure -$ .local/bin/make -j8 -``` - -For a general introduction to reproducible science as implemented in this -pipeline, please see the [principles of reproducible -science](http://akhlaghi.org/reproducible-science.html), and a -[reproducible paper -template](https://gitlab.com/makhlaghi/reproducible-paper) that is based on -it. - - - -Running the pipeline --------------------- - -This pipeline was designed to have as few dependencies as possible. - -1. Necessary dependencies: - - 1.1: Minimal software building tools like C compiler, Make, and other - tools found on any Unix-like operating system (GNU/Linux, BSD, Mac - OS, and others). All necessary dependencies will be built from - source (for use only within this pipeline) by the `./configure' - script (next step). - - 1.2: (OPTIONAL) 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 set directories outside the current directory. Please - read the description of each necessary input clearly and set the best - value. Note that the configure script also downloads, builds and locally - installs (only for this pipeline, no root previlages necessary) many - programs (pipeline dependencies). So it may take a while to complete. - - ```shell - $ ./configure - ``` - -3. Run the following command (local build of the Make software) 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 (you can see the number of threads available to your operating - system by running `./.local/bin/nproc`) - - ```shell - $ .local/bin/make -j8 - ``` |