[Treebase-devel] [help.nescent.org #7349] Re: upload broken on treebasedb-dev.nescent.org:80

[Jon A. v. R. <he...@ne...>]

Bill,

OK. I fixed it (again).  There are two things that need to be set for mesquite to work:

1)Add this to the Tomcat startup script:

# Headless mesquite needs a window server (a virtual one is OK)
export DISPLAY=localhost:1.0

2)  Add this to the CATALINA_HOME/conf/Catalina/localhost/treebase-web.xml file:
 
         <Environment name="tb2/MesquiteFolder" value="/home/treebasedev/mesquite-
2.01.tb"
             type="java.lang.String" override="false"
             description="Absolute path to the directory where headless Mesquite is unpacked on 
the host system."/>

I had changed the path for treebasedev home directory, and forgot to change it in treebase-
web.xml. It's in my notes now and I'll make sure its gets entered in the treebase wiki at 
Sourceforge.


BTW, the output form uploading the test file you sent me yesterday is:

File upload summary:
One matrix uploaded
One tree uploaded


The Parser Log:
Reading NEXUS file testfile.nex
Reading special block: DATA
Reading block: CODONS
Reading block: TREES
Reading block: ASSUMPTIONS
Reading block: Mesquite
NOTICE null
*************************
The current release version of Mesquite is 2.72 build 527 (the version you have installed is 
2.01). The latest version is downloadable at: 
http://mesquiteproject.org/mesquite/download/download.html
*************************

File reading complete (file testfile.nex)

-Jon

On Thu Feb 11 04:55:15 2010, wil...@ya... wrote:
> 
> On Feb 9, 2010, at 4:59 PM, Jon Auman wrote:
> 
> > Bill,
> >
> > This has been fixed. Mesquite requires that the tomcat startup
>    script export the display
> 
> Hi Jon,
> 
> Thanks for whatever you did... but I still can't seem to upload any
>    nexus files... I get a "File upload summary: No matrices or trees
>    uploaded" message.  I'm using the dev instance -- tried it with
>    both the port 80 and port 6666 builds.   Is there a particular
>    deployment that I should be testing?  (attached is a test file, if
>    you need something to try).
> 
> Bill
> 
> 
> 


-- 
Jon Auman
NESCent, Systems Administrator
jon...@ne...
919-627-2708



For more info:
Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7349 >