Hi Bjoern, I can see man years of effort being spent on solving this problem within Galaxy. I was going to title this email "Danger, Will Robinson", but I didn't want to be disrespectful. I think the path being embarked upon, tool dependency packaging, tool versioning, reproducibility, and long term archive of source tarballs is going to lead inevitably to creation of a new Linux distribution, which I guess will be called Galaxy Linux.
The packaging and archival you are talking about is exactly the service provided by a Linux distribution. There's well established infrastructure to handle this, and years of experience have gone into solving the problems well. Surely the number of Linux distributions in the world now exceeds 100, but I don't see that the world will become a better place if we increase that number by one more. We at AgResearch can't be alone in having to pick a Linux distribution to run from the short list supported by our hardware vendor. I can't see Galaxy Linux being on that list anytime soon. So we have to make Galaxy run on the particular distribution we have here. For us that's CentOS 6. Now, I see scary mention of platform independence as a goal for Galaxy packaging, which I interpret as "will run on any Linux distribution". I think that's essentially infeasible. All you can do is write install scripts which you hope are portable (by following as many best practices as you know about), and then work patiently with users on strange platforms, to adapt each install script to work on that platform also. I think this is not a good use of anyone's time. How many Linux distributions do the Galaxy community actually care about today? The RHEL family is surely important, as is Ubuntu LTS. Anything else? I'd be quite interested to understand this, as it provides a context for the discussion, and ensures we're not just solving a hypothetical problem. I'm just starting work on a native packaging infrastructure for Galaxy, that will enable tool dependencies to use defined versions of natively installed packages. That frees me up to make my packages work nicely on the RHEL family. It looks like the RPMs themselves (including SRPMs obviously) will be hosted by the CentOS project before too long. Once they're there, they can easily be archived forever. Anyone else on that platform is welcome to use the same infrastructure. Then, all we really need is someone to handle the packaging effort for the other major Linux distributions (a small number, I hope), and the problem is essentially solved. Getting the Bio-Linux team interested in multi-version packaging would be a great next step. I'll be posting here when I have progress to report on my native packaging effort. 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/
