Thanks for sharing this with the community!
As far as similar activities, we are actively working on a solution for
packaging and deploying tools. Enis can share more about that, it is what we
use already to automatically build our cloud images with all tools and data
Importantly, we are not using an existing package manager like RPM for (mostly)
two reasons. First, we're trying to avoid focusing specifically on redhat et
al. But more importantly, we want to avoid installing anything at the system
level. In particular because it is difficult to have multiple versions of the
same tool installed and usable at the same time. Instead, we are installing
everything in isolated directories like:
And adding the appropriate information to the environment at runtime based on
requirement tags in the tool config.
On Mar 2, 2011, at 12:38 PM, Leon Mei wrote:
> Dear colleagues,
> In order to ease administration on our servers running at VIB and
> NBIC, we will set up an RPM Repository for bioinformatics tools, the
> primary focus being NGS tools. The purpose is to come to a stable
> repository of easily installable packages for the common
> bioinformatics tools that can be used in a local Galaxy server.
> A list of tools under consideration can be found at
> So are there already similar activities going on? If yes, we would
> really love to hear your experience and probably work together on
> If you would like to join this effort and contribute into this
> repository, you are more than welcome to contact us as well!
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center (http://www.nbic.nl/)
> Skype: leon_mei Mobile: +31 6 41709231
> To manage your subscriptions to this and other Galaxy lists, please use the
> interface at:
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
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