My development cycle involves writing and testing my software and then run it in some sort of HPC cluster. My pipelines and scripts typically depend on thirty party software (samtools, bwa, picard, etc...)
Keeping those packages up to date in my machine is easy, it is not in the cluster. The main issue is that I don't have root privileges. Yes, I could rely on the sysadmins to install the software, but in my case that is a slow process. In addition, I need to keep things up to date and I want to do it quick.
I suspect I am not the only one that has run into this issue before. In an attempt to solve the problem, I wrote a simple package manager (biobrew). It helps but it expects some minimal packages to be already installed (like a compiler and some libraries). Those expectations (I think quite reasonable) are not always met. I am actually considering rebooting the biobrew project to completely bootstrap libraries and compilers.
I wanted to check with the biostar community: Have you experienced this problem in your environment? How did you solve it? Have you tried any user level package manager (preferably for linux)? Is biobrew something appealing to the community?
UPDATE (For those of you interested in having an up to date userland that you can control without requiring root privileges):
I want to report my success with gentoo prefix. It truly bootstraps a clean distribution at user level, including compiler and basic libraries. Highly recommended.