AutoPrime now resides on SourceForge.net

http://autoprime.de

Just a short note to our AutoPrime users: We finally moved the source code over to SourceForge.net. You can browse both the code for the main application as well as the part for the website of the service.

So far we just moved the files over to the cvs system and it will still need some minor cleanup to get development going over the new project site. At some point there will also be release packages available so that you can easily download and install the tool.

Primer_(molecular_biology) pcr rt-pcr science

Posted at: 19:59 | Permalink | category: /english/technical/projects

AutoPrime gets a forum

AutoPrime now has a support forum. This is currently not advertised on the main page since we still need to update the software. But feel free to use it if you prefer a forum over our support email address.

Primer_(molecular_biology) forum pcr rt-pcr science

Posted at: 08:44 | Permalink | category: /english/technical/projects

AutoPrime is back online

Just a short note to our AutoPrime users: The service is back online. It looks stable now and we hope that it will run without errors on the current server for the next few weeks. This is nevertheless a temporary solution and we are currently searching for a long term server solution.

I am myself not responsible for the service itself anymore and maintenance has been taken over by Felix. In case of problems with the primer design, please contact him directly or use the support@autoprime.de address.

Primer_(molecular_biology) pcr rt-pcr science

Posted at: 12:05 | Permalink | category: /english/technical/projects

Patches for a new horde driver sent upstream

The patches for the Horde Share driver that I created last week have seen some minor fixes and I did send them upstream now to get a first review from the horde devs. You'll find the patches attached to the ticket in the horde bug database or in the Kolab/Gentoo overlay.

horde patch

Posted at: 12:30 | Permalink | category: /english/technical/projects/kolab

goCluster updates

I gathered the support requests from the last two months and updated the goCluster page. The FAQ got a new item that explains linking gene identifiers and GO annotation in greater detail.

The main change to the package itself has been a new annotation class that can retrieve the annotation values from a look-up file. This is quite useful for all cases where you do not have an AnnBuilder meta package available for your microarray.

The package now also contains a change log where you'll find the latest fixes in detailed form. The newest version available in the bioconducter development section is now 1.5.1.

Posted at: 23:01 | Permalink | category: /english/technical/projects

Kolab currently stalled

My Kolab conversion to Gentoo has been stalled for a longer time now. I am currently programming some basic stuff that I feel I need before continuing on the project. This is progressing well and I hope to get back to Kolab in January. This hopefully coincides with the release of Kolab 2.1 which feature use of the autotools. This should also simplify the conversion.

Posted at: 09:37 | Permalink | category: /english/technical/projects/kolab

goCluster updates

Not that I would care about publications anymore but the paper on goCluster has been published in Bioinformatics and drew some additional users to the package which is nice.

So I added a project page for the software and this will hold some additional information on the package. For now I just added answers to some of the questions I got, a link to the newest version and the developer versions of the vignettes.

Since I wanted to check that the package is up-to-date for Bioconductor 1.7 (to be released soon) I rebuilt an R-development environment. This required the developer version of R so I adapted the Gentoo ebuild to the developer version. You can download it here. I'll provide no guarantee that this thing works. It installed without problems on my desktop but failed on my laptop (though I believe this was not related to the ebuild but some other problem on the machine).

Posted at: 22:58 | Permalink | category: /english/technical/projects

CVS updates

Integrated the latest kolab cvs changes into the code.

I started wrapping up cyrus imapd but it will still take a few days to be convinced that all kolab features work.

The problem with ownership of /var/lib/openldap-data after bootstrapping should not appear anymore and Henning helped me to identify another bug in the perl-kolab ebuild.

Posted at: 00:00 | Permalink | category: /english/technical/projects/kolab

Kolab updates

I broke the kolab-webadmin and the kolabd ebuilds last week. Fixed that today and they should both work again.

I addded all recent diffs from the kolab cvs which hopefully allows to create domain maintainers. I did not check this yet.

My postfix checks are running fine now and I updated the comments on the postfix page concerning changes in the configuration as compared to the original kolab.

I also modified the postfix users so that the special kolab users are not used anymore. When using these new templates you need to empty your postfix spool directory:

rm -rf /var/spool/postfix/*

Posted at: 15:17 | Permalink | category: /english/technical/projects/kolab

Fixing template configurations

Updated the ClamAV, Amavisd-new, and the Spamassassin templates for Gentoo. This brings me a step closer to finally fix postfix so that the Kolab server can actually send mail ... which is a nice feature for a mail server.

Posted at: 22:59 | Permalink | category: /english/technical/projects/kolab

Postfix needs correct kolab-resource-handlers

The postfix ebuild in portage seems to be ok and the newer version of postfix (2.2.2) contains the patches that are being applied in the older OpenPKG version. But the new version needs some fixes on the master.cf template included in kolabd.

The postfix part of Gentoo-Kolab does not work yet since the kolab-resource-handlers need to be fixed first.

Posted at: 18:17 | Permalink | category: /english/technical/projects/kolab

Postfix ebuild for Kolab

Postfix is slightly more difficult than I initially believed. The new postfix 2.2.2 package available from portage (Kolab uses 2.1.5) contains the patches included in the current Kolab version but there are some differences in the configuration files. So I will have to fix the templates for postfix.

Posted at: 14:32 | Permalink | category: /english/technical/projects/kolab