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Re: [Treebase-devel] TreeBASE <=> Mesquite interaction
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From: Rutger V. <rut...@gm...> - 2009-12-17 16:57:23
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Hi Wayne, thanks - I think we're not going to tinker with upgrading right now, though we definitely should later on. There are some situations where having a new mesquite on our server will significantly enhance the user experience (say, when they're uploading a massive set of bayesian trees) but right now we just want to roll out the Mission Accomplished banner and unveil TreeBASE2.0 Rutger On Thu, Dec 17, 2009 at 3:52 PM, Wayne Maddison <wma...@in...> wrote: > Hi Rutger, > Great! You might still want to look at MesquiteRunner, since it may turn > out that you could upgrade to Mesquite 2.72 via its methods. But, if your > current system ain't broke.... > Wayne > > At 5:58 PM +0000 16.12.2009, Rutger Vos wrote: >> >> Hi Wayne, >> >> it worked - hurrah! Thank you very much, high-fives all around. >> >> Rutger >> >> On Wed, Dec 16, 2009 at 3:28 PM, Wayne Maddison >> <wma...@in...> wrote: >>> >>> Rutger, >>> How about setting the static MesquiteModule.mesquiteDirectory before to >>> call >>> to Mesquite.main? >>> Wayne >>> >>>> Hi Wayne, >>>> >>>> On Tue, Dec 15, 2009 at 7:05 PM, Wayne Maddison >>>> <wma...@in...> wrote: >>>>> >>>>> This code is ancient -- probably has not been activated in 10 years! >>>>> Mesquite in general always knows where its home folder is, but we have >>>>> not >>>>> been trying server stuff. >>>> >>>> I know this code is ancient, which is why I was a little embarrassed >>>> to ask about it. Supposedly, Jin Ruan applied some slight patches to >>>> it to make it work with TreeBASE, but he didn't record anywhere what >>>> those changes were (and whether they're even still necessary: I notice >>>> a lot of work has gone into making mesquite more amenable to our sort >>>> of use cases). >>>> >>>> The hard part is that the server is quite a different environment that >>>> constructs its own class path and has its own way of loading classes. >>>> Also, the calling class lives inside a "war" file - a jar containing a >>>> web application - whereas mesquite lives inside >>>> $CATALINA_HOME/shared/classes, the location from whence shared classes >>>> are visible to web applications. >>>> >>>> Since "war" files are actually unpacked into a class folder the first >>>> time the server sees the archive I suppose I could copy the mesquite >>>> classes into that same folder structure and see what happens. Tomcat >>>> purists be damned. >>>> >>>>> mesquiteLocation.txt and the entries in Mesquite.xml don't help -- >>>>> they >>>>> are >>>>> a service to otehr programs. >>>> >>>> Ah, thanks, at least I can stop worrying about those then. >>>> >>>>> Is that the entire log file? >>>> >>>> The log file I sent you is the whole thing. >>>> >>>>> What version of Mesquite are you using? >>>> >>>> We're using version "2.01tb". >>>> >>>>> How exactly are you calling Mesquite? You might want to look into >>>>> svn.mesquiteproject.org, RMesquite, >>>>> src/java/mesquite/R/RCallsMesquite/lib/MesquiteRunner for an actively >>>>> developed class that instantiates and calls Mesquite. To tell you the >>>>> truth, now that I think about it, I'm not sure how this works -- I'm >>>>> not >>>>> sure how Mesquite knows its home directory if its in a different >>>>> classpath >>>>> than the one in which the class calling it lives. >>>> >>>> All we're doing is the following: >>>> >>>> Mesquite.main(new String[] {"-w"}); >>>> MesquiteProject project = >>>> MesquiteTrunk.mesquiteTrunk.openFile(pFile.getAbsolutePath()); >>>> >>>> I'll have a look at the R code, see if that gives me any pointers. >>>> >>>> Thanks! >>>> >>>> Rutger >>>> >>>> >>>>>> Hi Wayne, >>>>>> >>>>>> I'm having trouble launching mesquite programmatically as treebase's >>>>>> nexus file parser. Try as I might, the log keeps showing that it >>>>>> cannot find the Mesquite_Folder: it wants me to show where the >>>>>> manuals >>>>>> is located. Could you give me a hint as to which of the following >>>>>> moving parts are involved: >>>>>> >>>>>> * ~/Mesquite_Support_Files/Mesquite_Prefs/mesquiteLocation.txt - I >>>>>> set >>>>>> this to the right location >>>>>> >>>>>> * ~/Mesquite_Support_Files/Mesquite_Prefix/Mesquite.xml - I set >>>>>> mesquiteHeadlessPath and mesquitePath to the right location >>>>>> >>>>>> * system property "mesquite.folder_dir" - I set this to the right >>>>>> location >>>>>> >>>>>> What else can I do? Is there a programmatic way to set this? I'm >>>>>> hoping to have overlooked a Mesquite.setMesquiteDirectory() method, >>>>>> but there are probably good reasons why that doesn't exist. Can I >>>>>> pass >> >> >>>> it to the main method? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> Rutger >>>>>> >>>>>> -- >>>>>> Dr. Rutger A. Vos >>>>>> School of Biological Sciences >>>>>> Philip Lyle Building, Level 4 >>>>>> University of Reading >>>>>> Reading >>>>>> RG6 6BX >>>>>> United Kingdom >>>>>> Tel: +44 (0) 118 378 7535 >>>>>> http://www.nexml.org >>>>>> http://rutgervos.blogspot.com >>>>>> >>>>>> Content-type: application/octet-stream; name=Mesquite_Log >>>>>> Content-disposition: attachment; filename=Mesquite_Log >>>>>> X-Attachment-Id: f_g38tnpcj0 >>>>>> >>>>>> Attachment converted: Thrandina:Mesquite_Log 78 ( / ) >>>>>> (0078D979) >>>>> >>>>> >>>>> -- >>>>> -------------------------------------------------------- >>>>> Wayne Maddison >>>>> Professor and Canada Research Chair >>>>> Depts. of Zoology and Botany and >>>>> Biodiversity Research Centre >>>> >>>> > & Director >>>>> >>>>> Beaty Biodiversity Museum >>>>> 6270 University Boulevard >>>>> University of British Columbia >>>>> Vancouver, BC V6T 1Z4 Canada >>>>> >>>>> email: wma...@in... FAX: +1 604 822-2416 >>>>> >>>>> Mesquite: http://mesquiteproject.org >>>>> MacClade: http://macclade.org >>>>> Salticidae: http://salticidae.org >>>>> Tree of Life: http://tolweb.org >>>>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >>>>> Home page: http://salticidae.org/wpm/home.html >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading >>>> RG6 6BX >>>> United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://www.nexml.org >>>> http://rutgervos.blogspot.com >>> >>> >>> -- >>> -------------------------------------------------------- >>> Wayne Maddison >>> Professor and Canada Research Chair >>> Depts. of Zoology and Botany and >>> Biodiversity Research Centre >>> & Director >>> Beaty Biodiversity Museum >>> 6270 University Boulevard >>> University of British Columbia >>> Vancouver, BC V6T 1Z4 Canada >>> >>> email: wma...@in... FAX: +1 604 822-2416 >>> >>> Mesquite: http://mesquiteproject.org >>> MacClade: http://macclade.org >>> Salticidae: http://salticidae.org >>> Tree of Life: http://tolweb.org >>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >>> Home page: http://salticidae.org/wpm/home.html >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com > > > -- > -------------------------------------------------------- > Wayne Maddison > Professor and Canada Research Chair > Depts. of Zoology and Botany and > Biodiversity Research Centre > & Director > Beaty Biodiversity Museum > 6270 University Boulevard > University of British Columbia > Vancouver, BC V6T 1Z4 Canada > > email: wma...@in... FAX: +1 604 822-2416 > > Mesquite: http://mesquiteproject.org > MacClade: http://macclade.org > Salticidae: http://salticidae.org > Tree of Life: http://tolweb.org > Beaty Biodiversity Museum: http://beatymuseum.ubc.ca > Home page: http://salticidae.org/wpm/home.html > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
