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Two possibilities:
A lot of widely-used programs have been installed globally (BLAST, tophat, bowtie, samtools, …)
apt-get won’t do it.
Possibilities:
Since your home directories are available on all nodes, any program you install locally will automatically be available to you on the compute nodes. (This is not always true with apt-get installations, as they sometimes go into /usr/bin which is not shared across nodes.)
This can be quite simple, or a nightmare of dependencies.
cd source_dir make
./configure -prefix=$HOME make install
apt-get source package-name tar -zxf package-name.tar.gz cd package-dir ./configure -prefix=$HOME make install
You can install conda in your own home directory and then use it to install a specific version of python or R (for instance).
For instance, to install R 3.6.1 (currently):
conda create -n r-test r-base r-tidyverse r-rlang ... conda activate r-test
Using a Singularity container allows you to have complete control over your environment and what is installed, and allows you to share that environment with others.
See the page on Using Singularity.