Hi Mark & Mark, This is the list of command files that we're currently using on the portal (Lucie keeps this list in cipresweb/cipres-web/src/main/resources/conf/mapping.txt) and the status of my attempt to convert them to our new xml format that can be used to initialize guigen. It looks like we need to modify the uixml files for paup (improve and infer) and for raxml. I'm happy to make the changes, but would appreciate it if you'd look at each of the issues I encountered below and give me some advice. Thanks, Terri garli.xml OK paup_ratchet_improve.xml 1. The command file sets "maxTrees=210", "increase=no" and "multrees=no", but the uixml doesn't let us set maxTrees or increase unless multrees=yes. 2. The command file sets "addseq=random" but addseq isn't a parameter in the uixml. Should it be? Should we also add nreps, as in the infer uixml? ### 8/27/07: OK. Per Mark's email, created parameter_files/paup_ratchet_improve.xml that doesn't have settings for maxTrees, increase, addseq nor reps. paup_ratchet_infer.xml 1. Same issue as with paup_ratchet_improve.xml regarding maxTrees, increase and multrees. ### 8/27/07: OK. Per Mark's email, created parameter_files/paup_ratchet_infer.xml that doesn't set maxTrees and increase. raxml-aa.xml 1. The command file sets "-m PROTGAMMAWAGF", but this isn't one of the models allowed in the uixml. It looks like our current uixml only supports the nucleotide models. 2. The command file specifies "-c 25", but running "raxml -h" seems to indicate that "-c" isn't relevant with this model. Should we have separate uixml files for aa and rna/dna data for the portal? Should we add all the all models or is there some reason not to do this on the portal? ### 8/28/08: OK. Mark committed a new version of raxml_improve.xml uixml that lets you set all the models; I created parameter_files/raxml-all.xml using the new uixml to set PROTGAMMAWAGF. raxml.xml OK rid3-rax-6.25-pct.xml rid3-rax-12.5-pct.xml rid3-rax-16-pct.xml rid3-rax-25-pct.xml rid3-rax-50-pct.xml OK, except that command file specifies GTRGAMMA and "-c 25" and I don't think "-c 25" is allowed with this model. Remove it? ### 8/27/07: Per Mark's email, created versions in parameter_files w/o the "-c 25". rid3-rax-aa-6.25-pct.xml rid3-rax-aa-12.5-pct.xml rid3-rax-aa-16-pct.xml rid3-rax-aa-25-pct.xml rid3-rax-aa-50-pct.xml Same issue as with raxml-aa.xml. ### 8/28/08: OK. Mark committed a new version of raxml_improve.xml uixml that lets you set all the models; I created parameter_files/rid3-rax-aa-*-pct.xml using the new uixml to set PROTGAMMAWAGF. ========================================================================================================= Mark's reply: ========================================================================================================= Hi Terri, Thanks for doing that. I am sure that it was tedious. On Aug 24, 2007, at 4:09 PM, Terri Liebowitz wrote: > Hi Mark & Mark, > > This is the list of command files that we're currently using on the portal (Lucie keeps this list in > cipresweb/cipres-web/src/main/resources/conf/mapping.txt) and the status of my attempt to convert > them to our new xml format that can be used to initialize guigen. > > It looks like we need to modify the uixml files for paup (improve and infer) and for raxml. I'm > happy to make the changes, but would appreciate it if you'd look at each of the issues I > encountered below and give me some advice. > > Thanks, > Terri > > garli.xml > OK > > paup_ratchet_improve.xml > 1. The command file sets "maxTrees=210", "increase=no" and "multrees=no", but the uixml > doesn't let us set maxTrees or increase unless multrees=yes. You should be able to remove the maxtree=210 now. It used to be required for the ratchet impl because I read in the results from all 200 ratchet iterations to find the best tree. I have changed the impl to make it more robust to the user tweaking the maxtrees (the first impl would have broken if the user set too low a maxtrees setting). This points to a weakness in our current system, I don't really read and parse the PAUP commands. I just pass them along to paup. So the wrapper impl can conflict with user settings. I think that this instance of this problem (maxtrees and ratchet) has been fixed. > > 2. The command file sets "addseq=random" but addseq isn't a parameter in the uixml. > Should it be? Should we also add nreps, as in the infer uixml? Addseq shouldn't be in a tree improver (though it won't hurt). It came from copying at tree infer command file and tweaking. > > > paup_ratchet_infer.xml > 1. Same issue as with paup_ratchet_improve.xml regarding maxTrees, increase and multrees. Same answer, as for improver -- it should be safe to remove the maxtrees=210 (note this should not change the analysis, because it was a setting that PAUP ignores, so Lucie will not need to rebenchmark after this change). > > > raxml-aa.xml > 1. The command file sets "-m PROTGAMMAWAGF", but this isn't one of the models allowed in the > uixml. It looks like our current uixml only supports the nucleotide models. That is correct. I was hoping that we would add some switch logic based on datatype. But in the short term I should add the aa models to the ui_xml > > > > 2. The command file specifies "-c 25", but running "raxml -h" seems to indicate that "-c" > isn't relevant with this model. It actually is relevant. When I add the aa models to the uixml, I'll need to make sure to change the availability-test for the -c param. It is currently set to look for the DNA rate heterogeneity models only (which is why it thinks that -c is not applicable). Short term fix is to comment out the test. > > Should we have separate uixml files for aa and rna/dna data for the portal? I can't think of a program that would need a separation. I think they all treat RNA as if it were DNA during the analysis. > > > Should we add all the all models or is there some reason not to do this on the portal? I'd vote that we add all of the models if it is not too much of a pain. > > > > raxml.xml > OK > > rid3-rax-6.25-pct.xml > rid3-rax-12.5-pct.xml > rid3-rax-16-pct.xml > rid3-rax-25-pct.xml > rid3-rax-50-pct.xml > OK, except that command file specifies GTRGAMMA and "-c 25" and I don't think "-c 25" is allowed > with this model. Remove it? Yes, remove it > > > > rid3-rax-aa-6.25-pct.xml > rid3-rax-aa-12.5-pct.xml > rid3-rax-aa-16-pct.xml > rid3-rax-aa-25-pct.xml > rid3-rax-aa-50-pct.xml > Same issue as with raxml-aa.xml. > Same fix, will work here. Cheers, mark Mark Holder mtholder@ku.edu ============================================== Department of Ecology and Evolutionary Biology University of Kansas 6031 Haworth Hall 1200 Sunnyside Avenue Lawrence, Kansas 66045 lab phone: 785.864.5789 alt. phone: 785.371.4666 fax (shared): 785.864.5860 ==============================================