We are attempting version-specific packaging of bioinformatics software, such that multiple versions of the same app can exist on the same host.
Has Debian-Med encountered the need for this sort of thing from others from the scientific community? Do you have recommendations for how best to approach the problem in a way which will help us, and let us contribute back to you, most effectively? BACKGROUND: The Genome Institute is attempting to shift to using formal packaging for internal software distribution across our compute cluster. All of our blades run Ubuntu Lucid now, so we have an interest in getting Debian packages for all of the popular bioinformatics tools we use, or helping to make them. Our biggest difficulty is that our pipelines expect to produce reproducible results over time, and as such only call "versioned executables". We currently custom compile everything, and install each version next-to each other. The actual executable in the PATH is something like "cufflinks1.2.0", which prepends to the PATH where that code exists, and executes the "cufflinks" binary in that directory. In many cases the apps we are packaging are apps which you have already packaged, and we only need to change things for the per-version packaging. In other cases you have an older version of the code. In others, you have not packaged it at all. Our current trajectory is to hand-repackage whatever we depend on making the version number part of the package name, and formalizing the above shell-wrapper strategy. For our first few attempts we use etc-alternaives to manage a symlink with the generic app name. Upgrades will not happen as a user might expect, since each version is its own package, but we tentatively planned to make a meta-package with a name like "cufflinks-versioned" which depends on a regularly changing "cufflinksN.N.N" package, and would create the common user experience for anyone who did not request a specific version. Thanks in advance for your advice, Scott -- Scott Smith Manager, Application Programming and Development Analysis Pipeline The Genome Institute Washington University School of Medicine -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
