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 also looked into Gentoo prefix but it did not quite fit my needs (I may have to revisit the project). Another option could be netbsd's ports, but I haven't explored it, yet.
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?
Thanks.
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.
And there is also a Linuxbrew, which seems to bring much of Mac Homebrew and what you hoped to accomplish using bio.brew.
Same problem here - users have to build, install their own software. The system uses "modules" (http://modules.sourceforge.net/ ) for managing tools. I create module configuration files for my lab with custom installations of R and other tools the admin won't touch because of reasons.
dotkit is a similar tool which broad institute is using.