How to install multiple software versions on the same computer?

Question

[Trombone Engineer]

For software that I have been installing and trying to use, I often see dependencies that require a certain version of software that is not the most current version. How reasonable is it to install multiple versions of software so that I have the most recent version, in addition to an older version that other software requires? The software I would like to have multiple versions of include Python, Cytoscape, and Biom Format. All of these software sources still have the past versions I am interested in available from their websites. When I was reading forum posts related to installing Biom Format for QIIME and PICRUSt, I saw some mention of using virtual sessions within a single computer to install multiple versions of Biom Format. I have been able to install most of the software I have needed on my Ubuntu computer, but would it be possible and reasonable for me to install multiple versions of Cytoscape or Biom Format on my computer?

[fanli.gcb]

I've been using conda to manage QIIME versions. Since most/all of what you seem to want are Python, that might be a useful approach.

Answer 1

[GenoMax]

Look into modules for keeping multiple versions of software available.

Answer 2

[Alex Reynolds]

Our lab uses modules to maintain different versions of tools. When we launch cluster tasks, it's easy to set up the environment needed to run the task with the specific versions of software needed.

Answer 3

[h.mon]

For most software, you can have multiple versions. As others pointed, you can use a package manager like {home,linux}brew or conda, which will allow multiple versions of the same software. Most bioinformatics packages are distributed as source, then usually you just have to read the instructions and tweak a bit. For example, most packages will install with ./configure && make && make install, you just have to (generally) run ./configure --prefix=path/to/specific/version. Python packages are easily managed with virtualenv. To manage these multiple versions, for the most part you have to set up PATH and sometimes LD_LIBRARY_PATH variables - modules is a fancy way of doing this and hiding the complications from regular users.

Cytoscape, on the other hand, I do not know, as it creates a .cytoscape folder, and different versions may be incompatible (versions 2 and 3 are).