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@@ -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'. |