Dear all, After a few modifications to BiNGO.java and Module.java, removing all annoying GUI stuff, our program can now run in headless mode on the cluster nodes... I added RunHeadless.java in the repository (Release1 branch). However, I couldn't commit the other modified .java files (so it won't work yet), I got svn 'out of date' errors while the files were minutes old. Eric, any ideas ? Also, Tom, should I commit the modified TreeNode.java (for handling the NaN's) and ModuleNetwork.java (there was still this bit of code for handling the CS module overlap in there) to Release1 or not, what do you think ? And are there any other changes to the trunk code that should be added to Release1 (to avoid having versions that diverge too much) ? Cheers, Steven -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group Ghent University / VIB Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3692 fax: +32 9 331 3809 email: stmae@psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================
On Thursday 24 August 2006 19:06, Steven Maere wrote:
Dear all,
After a few modifications to BiNGO.java and Module.java, removing all annoying GUI stuff, our program can now run in headless mode on the cluster nodes... I added RunHeadless.java in the repository (Release1 branch). However, I couldn't commit the other modified .java files (so it won't work yet), I got svn 'out of date' errors while the files were minutes old. Eric, any ideas ? Also, Tom, should I commit the modified TreeNode.java (for handling the NaN's) and ModuleNetwork.java (there was still this bit of code for handling the CS module overlap in there) to Release1 or not, what do you think ? And are there any other changes to the trunk code that should be added to Release1 (to avoid having versions that diverge too much) ?
Cheers,
Steven
Hi Steven & co, I think the main idea of the Release version is to contain the minimal subset of our code that is needed to reproduce the results we present in our paper, so we can refer whoever is interested to this version. What seems most important to me now is that all major improvements are also contained in the trunk version for our future work. The reduction trunk -> release is something we'll still have to work on quite a bit as there is a lot of code in almost all classes that is not needed in the release version (although I believe Eric has already weeded out some stuff?). That said, I don't think there have been any other changes in trunk lately (I'd check svn log on trunk and release though to be sure). Cheers, Tom
Indeed I did quite some modifications in the Release1 directory, suppressing the stuff that was not necessary (particularly in the ModuleNetwork class). I would suggest to incorporate changed code by hand in the release1 so that we don't have to clean everything again. Probably we can discuss that further at the meeting this afternoon. Eric Tom Michoel wrote:
On Thursday 24 August 2006 19:06, Steven Maere wrote:
Dear all,
After a few modifications to BiNGO.java and Module.java, removing all annoying GUI stuff, our program can now run in headless mode on the cluster nodes... I added RunHeadless.java in the repository (Release1 branch). However, I couldn't commit the other modified .java files (so it won't work yet), I got svn 'out of date' errors while the files were minutes old. Eric, any ideas ? Also, Tom, should I commit the modified TreeNode.java (for handling the NaN's) and ModuleNetwork.java (there was still this bit of code for handling the CS module overlap in there) to Release1 or not, what do you think ? And are there any other changes to the trunk code that should be added to Release1 (to avoid having versions that diverge too much) ?
Cheers,
Steven
Hi Steven & co,
I think the main idea of the Release version is to contain the minimal subset of our code that is needed to reproduce the results we present in our paper, so we can refer whoever is interested to this version. What seems most important to me now is that all major improvements are also contained in the trunk version for our future work. The reduction trunk -> release is something we'll still have to work on quite a bit as there is a lot of code in almost all classes that is not needed in the release version (although I believe Eric has already weeded out some stuff?). That said, I don't think there have been any other changes in trunk lately (I'd check svn log on trunk and release though to be sure).
Cheers, Tom _______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
participants (3)
-
Eric Bonnet -
Steven Maere -
Tom Michoel