Instructions necessary to produce the results discussed in the paper, from download of primary data to computations and tables/figures, are given in a sequence of scripts and Jupyter notebooks as recored in file ./xdoitall. Each individual analysis should run with no problem on a laptop or desktop computer, although reproducing all the basic analyses requires about 200 GB of free disk space for temporary storage of raw and intermediate data files (the large-scale genome compactness analysis summarizing different clades of species in the ./taxa subdirectory would require another 350-400 GB).
Some long UNIX commands in this documentation are split across multiple lines.
This is done for the sake of readability.
The use of the backslash (\) character indicates that the following line is
part of the same command.
For example, the command
rws fidibus --workdir=data \
--numprocs=2 \
--refr=Scer,Cele \
download prepis identical to the command
rws fidibus --workdir=data --numprocs=2 --refr=Scer,Cele download prepThe easiest way to run the Juypter notebooks described here is by creating a suitable python environment. The following provides one way of doing this:
#Installation of prerequisites (shown for Fedora Linux; other systems will have
#equivalent pacckage managing tools):
sudo dnf install libXcomposite libXcursor libXi libXtst libXrandr \
alsa-lib mesa-libEGL libXdamage mesa-libGL libXScrnSaver
#Download and run the Anaconda3 installer from https://www.anaconda.com/, e.g.:
#
wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
bash ./Anaconda3-2021.05-Linux-x86_64.sh
\rm ./Anaconda3-2021.05-Linux-x86_64.sh
#In a new shell:
#
conda config --set auto_activate_base False
conda deactivate
#In a new shell:
#
conda --version
conda info --envs
conda create --name iLoci biopython pycurl pyyaml pytest pytest-cov \
jupyter pandas seaborn nb_conda_kernels ipykernel r-irkernel
conda activate iLociand now
jupyter notebook