There is a similar but probably larger set of Debian packages available via Debian-Med and Bio-Linux too. The catch here is can you install arbitrary versions of a tool in parallel? And I think the answer sadly is no.
This is the crucial concern for us. The standard OS packaging approaches (RPM and DEB) do not support this except very poorly. This is something we absolutely need. There are other package managers that do a better job (I'm quite fond of Homebrew on OS X, NIX also looks nice) but would add more dependencies.
There are possibilities here, similar to things I've already been doing in my RPM packaging.
If you want to install multiple versions side by side, when you (or more
On Thu, Aug 29, 2013 at 4:17 PM, Guest, Simon <Simon.Guest@agresearch.co.nz> wrote: likely, me) are making the packages, you just make the version number part of the package name, and install it out of the way somewhere (e.g. /usr/libexec/tophat-2.0.9, rather than /usr/bin). Then, the package can provide a versioned environment module as per http://modules.sourceforge.net/. There could be a non-versioned environment module which just gives you the latest and greatest version. So: This is the same thing that the tool shed does. From Greg: "Following best practices, repositories of type Tool dependency definition are named something like package_<name>_<version> (e.g., package_amos_3_1_0, package_ape_3_0, package_atlas_3_10, etc) and are contained in the Tool Dependency Packages category in the Tool Shed. The name of the repository contains the package name as well as the version because the contents of the repository must contain only the recipe for installing that specific version of that package. If a new version (say 3.1) of the ape package is introduced some time in the future, then a new repository named package_ape_3_1 should be created to contain the recipe for installing that version." Tool dependency definition repositories may only have one installable revision. Toolshed has some advantages over OS packages, but I do not understand why handling of multiple versions is considered by some among these.
$ module load tophat/2.0.9 # now that version is on the path
# start again ... $ module load tophat # the latest and greatest tophat becomes available
We've been using this to provide multiple versions of small tools, but
also bigger things like a version of Python more recent than the system one. (Software Collections may be better for the latter though - https://access.redhat.com/site/documentation/en-US/Red_Hat_Developer_Toolset... )
I'm willing to explore the feasibility of overhauling the AgResearch RPM
repo to support multiple versions of packages in this or a similar way if there's interest. There's clearly value in being able to select what version of a tool you run, if it can be done in a way that doesn't encumber those who just want to run a recent good version.
Is there interest in this approach? (Note: I'm not committing to doing it
just yet.)
cheers, Simon
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