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installation
Here we will cover how to install smudgeplot. The first step is the same regardless of the type of installation you wish to do - download this repository
git clone https://github.com/tbenavi1/smudgeplot
cd smudgeplot
You need to install the smudgeplot R package for plotting and make sure that some python dependencies (numpy and scipy) are present.
Rscript install.R
pip3 install -r requirements.txt
Then you just need to install following two scripts:
install -C exec/smudgeplot.py /usr/local/bin
install -C exec/smudgeplot_plot.R /usr/local/bin
smudgeplot.py is a python script that is the user interface and smudgeplot_plot.R is an R script for plotting internally called by smudgeplot.py, but accessible to user if desired. To check if the installation is working run
smudgeplot.py --version
if you see the version of smudgeplot printed, everything should be alright.
If the R is correctly configured, you should be able to install the R library directly exactly the same as for the global installation.
Rscript install.R
The python requirements should be installed already, these are very standard libraries that should be available on every cluster. If not, the dependencies can be installed in a virtual environment.
Finally, you probably won't be allowed to install the script to /usr/local/bin, then you can install them somewhere where your console will see it (i.e. on one of the places specified in environmental variable $PATH). If you are not sure what I just asked you to do, check the explanation of veriable PATH on wikipedia and this page that says how to change it or perhaps ask someone around.
install -C exec/smudgeplot.py /home/my_account/bin
install -C exec/smudgeplot_plot.R /home/my_account/bin
where /home/my_account/bin must be mentioned in PATH. Again, you can verify that it works
smudgeplot.py --version