Show that bioconda recipes are constantly updated

[HenningTimm]

For me, one of the main selling points (for lack of a better word) of bioconda is the availability of recent versions of software. When bioinformatics software is available in Linux package managers like apt, apart from the usual problem of not having root access to install it, it tends to be horribly outdated. Can we pour this into a graphic somehow? Some interesting parameters might be:

• How many updates do existing recipes receive? (This could be evaluated by counting the different version numbers available or commits changing the version number. I am not sure what is representative for actual "updates" to a recipe.
• If a bioconda package is also available as a ubuntu package, is the bioconda version older/ the samer/ newer than the ubuntu version? This could be done for any other distribution and/ or package manger.
• It would be awesome to find out how many recipes are at the most recent version of the respective software, but I do not see an easy way to check this.

I will try to implement this if you think this would be helpful.

[johanneskoester]

Yes, that would be awesome!! Thanks!

[epruesse]

Bioconda is intrinsically more up-to-date than Distros following an update schedule. The ordinary distribution package managers have to do that, because without the environment approach, the dependency network becomes unmanageable.

Arguing the other way around, though, I think having a notification scheme similar to what Debian uses (regex based scraper) would be useful for Bioconda, to make sure packages stay up-to-date. Such a tool would also provide the data you want -- time-to-package from date of release. It should be easy enough to do generically for things hosted on github and bitbucket, a little more complicated for sourceforge packages, and requiring a section in meta.yaml for self-hosted things.

[jerowe]

I am a pretty terrible writer, but I would like to chime in from the perspective of support staff.

Conda/Bioconda is so far beyond any other build system I have had to support. It is incredibly user friendly, from users that are just logging into an HPC terminal for the first time to power users setting up their own analyses.

If you install things through a distro (apt-get/yum) everything gets thrown in a global area. This does not work for bioinformatics softwares, because there are insane and often conflicting dependency trees. Say I am supporting 1 group or lab that needs R 3.1, and another group that needs R 3.2. This would be very difficult, if not impossible, using a distro. However, with the conda design that packages should be self contained and isolated this is possible.

Bioconda really shines with its community. I tend to install software, but rarely use it. I have built several softwares that did not work out of the box, but luckily the community chimed in and either I fixed it or another bioconda member fixed it.

The moral of the story is keep your admins happy. ;-)