> > 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 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: $ 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/1/html/Software_Collections_Guide/) 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 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/