Hi Raphael, Glad to hear the upgrade worked well for you!
In principle biojava-trunk does compile most of the time. (see http://ccpublic.rcsb.org/cruisecontrol/buildresults/biojava ). However, I just re-built it and you are right, something is wrong. Seems we are getting rather inconsistent responses from a Uniprot web service request. If this does not resolve itself soon, I'll contact Uniprot to take a look. I suspect one of their servers is down... Thanks and best wishes, Andreas On Wed, Feb 12, 2014 at 7:17 AM, Raphael André Bauer < [email protected]> wrote: > Hi, > > > five years ago I finished my PhD thesis. One part of the thesis was an > algorithm called "LaJolla". It was able to compute structural > alignments of RNAs (which was pretty new at that time) and proteins > (which was not new). LaJolla was written in Java 1.6 and used BioJava > 1.6 (and some other now outdated stuff). Biojava wasn't even available > from Maven at that time, which made building the thing a bit > cumbersome. LaJolla uses BioJava internally to parse PDB files and in > the calculation of the shift and rotation matrices for the structural > alignment. > > Now I had some time to upgrade LaJolla. Moved it from svn / > sourceforge to github and especially made it build again with latest > stuff like Maven 3.11, BioJava 3.0.7. I Also released version 2.2 - > ready to use on the command line. > > The experience of upgrading LaJolla from Biojava 1.6 to BioJava 3.0.7 > was really smooth. There were some changes I had to make, but it took > not to long how to figure out how stuff in 3.0.7 works. LaJolla builds > smoothly and even has its own CI server. Now LaJolla no longer is a > dead project from a code perspective. > > That means many things. But it especially means that the BioJava > community did a really great job on running the project over the last > couple of years. Thanks for that and keep up the awesome work! > > Because I am no longer working in academia I am not sure were the > project goes to. But as it's now on github it's a lot easier to > collaborate. If you have ideas let me know :) Pull requests are always > welcome! (http://github.com/raphaelbauer/lajolla). > > > Cheers, > > Raphael > (ps. I was not able to build BioJava master on my machine - which > makes sense, because CI also says the build is failing. But that's > hopefully just temporary.) > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
