[Gramene] gramene CVS and navigation bar

[Ken Youens-Clark]

On Oct 2, 2008, at 3:01 PM, Jonathan Arvisais wrote:

> Hi,
>
> I'm following instructions from the file README.ensembl found in
> gramene-28.0.0.tar.gz
>
> It says:
> «
> 3. Check out the gramene project from CSHL's CVS repository. You may
>   need to use the cvs-tmp dir, and then copy back into
>   /usr/local. The following example checks-out the build28-branch;
>
>   $ cvs -d formaggio.cshl.org:/usr/local/cvs_repository \
>     co -r build28-branch gramene
> »
>
> But running this CVS command returns this error:
>
> connect to address 143.48.31.42: Connection timed out
> Trying krb4 rsh...
> connect to address 143.48.31.42: Connection timed out
> trying normal rsh (/usr/bin/rsh)
> formaggio.cshl.edu: Connection timed out
> cvs [checkout aborted]: end of file from server (consult above  
> messages if
> any)
>
> I got the same error when I tried to install release 27. It's like  
> there
> is no CVS server running on this machine. My computer is connected
> directly to the internet and I can download files from any other CVS
> repositories without any problem.

Jonathan,

As you have downloaded the Gramene 28 tarball, you can skip this  
step.  You should have everything you need.

> I finished installing Gramene Core. But when I open the 'Home' page
> (index.shtml) the Gramene navigation bar is not displayed. But when  
> I open
> any other page (ex.: protein/index.html), it's displayed.
> Also, when I simply make a copy of index.shtml called index2.html (not
> shtml), and open index2.html, the navigation bar is displayed. There  
> may
> be an issue with the server not adding the navigation bar on SHTML  
> pages.
> I renamed the file index.shtml to index.html and restarted the Apache
> server, but it still looks for the file index.shtml even when I enter
> index.html in the URL.

There is a RewriteRule in place that sends "index.html" to  
"index.shtml."  I put this in place last build, but you can delete  
this line from the "httpd.conf" to stop that behavior:

   RewriteRule ^/index.html /index.shtml [R]

I'm not sure why the "index.shtml" page isn't being wrapped with the  
headers and footers.  Maybe eliminate the RewriteRule and see what  
that does?

ky