Hi James, On 2 March 2011 19:44, James Taylor <james@jamestaylor.org> wrote:

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.

Thank you for your feedback. We'd be interesting in seeing what you do for your cloud images. I do think that we can achieve the same as you do with RPMl, if we design our repositories and the rpms well. My idea is that we would have two repositories: 1. Repository with the latest versions 2. Repository with versioned RPMs The repository with the latest versions is used for people who just want to always have the latest versions, the repository with the versioned RPMs is used if you want to pin to specific versions. The versioned repository could install with the same $GALAXY_APPS/package/version/ structure as you use. The nice thing about have RPM packages is that you know exactly which version is installed, and that the package management system is already there to take care of dependencies. We do consider to provide packages for other distributions later, but serving our own services is what we start with, and those are Red Hat. Actually, since RPM is the packaging format chosen in the Linux Standard Base any compliant distribution (and all major ones are) should be able to install RPM packages if we take care to provide the correct dependencies. (i.e. -compat packages for things that are missing) With kind regards, David van Enckevort

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

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-- David van Enckevort Project Leader biobanking taskforce Software Integration Engineer BioAssist mob: +31 6 543 32 276 tel: +31 24 36 19 500 fax: +31 24 89 01 798 E-mail: david.van.enckevort@nbic.nl Skype: enckevort76 Netherlands Bioinformatics Centre 260 NBIC P.O. Box 9101 6500 HB Nijmegen