Hi Leon,
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 installed.
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:
$GALAXY_APPS/package/version/
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 https://wiki.nbic.nl/index.php/NBIC_%26_VIB_Bioinformatics_RPM_Repository
So are there already similar activities going on? If yes, we would really love to hear your experience and probably work together on this.
If you would like to join this effort and contribute into this repository, you are more than welcome to contact us as well!
Thanks, Leon
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231
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-- jt
James Taylor, Assistant Professor, Biology / Computer Science, Emory University