diff options
Diffstat (limited to 'README')
| -rw-r--r-- | README | 117 |
1 files changed, 14 insertions, 103 deletions
@@ -1,7 +1,7 @@ -Reproduction pipeline for XXXXX. +Reproduction pipeline for XXXXXXX -For a general introduction to reproducible science as done here, please see -the link below: +For a general introduction to reproducible science as implemented in this +pipeline, please see the link below: http://akhlaghi.org/reproducible-science.html @@ -10,112 +10,23 @@ the link below: Running the pipeline ==================== -To reproduce the results, please take these steps in order: +1. Necessary dependency: LaTeX. -1. Make sure you have the dependencies (below). + Other than LaTeX, this pipeline just needs some basic building tools + that are already present if you have ever build a software from source + (Tar, C compiler, and Make). The pipeline will build its own + dependencies when you run `./configure'. -2. Configure/set your top-level directories with the command below. It is +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 everything on 8 threads. If your - CPU has a different number of threads, change the number. +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. - $ 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. - - - Bash - ---- - - Bash is the most common "shell" or command-line manager and available in - almost all systems (even if not the default). It doesn't need to be the - default for this pipeline to run. - - - flock - ----- - - This is a small program to manage file locks from the command-line. It is - available in all GNU/Linux distributions. For those operating systems - that don't have it, an implementation that is easy to install is - available in the link below. - - https://github.com/discoteq/flock - - - - 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. - - - - 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'. + $ .local/bin/make -j8 |