[Gramene] gramene CVS and navigation bar

[Jonathan Arvisais]

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.

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.
The file cmap.conf/global.conf already contains the line "page_object 
Gramene::Page".

Thanks!

_______ 
Jonathan Arvisais 
Programmeur Informatique
T: (450) 358-2621 x224 
DNA Landmarks Inc. 
84 Richelieu 
St.-Jean-sur-Richelieu, J3B 6X3
Québec, Canada 
jonathan.arvisais at dnalandmarks.ca
www.dnalandmarks.ca 
DNA LandMarks 
une compagnie de BASF Plant Science 
a BASF Plant Science company 



Ken Youens-Clark <kclark at cshl.edu> 
2008-09-16 18:10

To
Jonathan Arvisais <Jonathan.Arvisais at dnalandmarks.ca>
cc

Subject
Re: [Gramene] gramene CVS






On Sep 11, 2008, at 10:00 AM, Jonathan Arvisais wrote:

>
> Hi,
>
> I'm installing gramene27 so I downloaded this file:
> 
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/software/gramene-27.0.0.tar.gz

>
> Inside this archive, the file README.ensembl says I should download 
> the gramene project from CSHL's CVS repository using this command:
> $ cvs -d formaggio.cshl.org:/usr/local/cvs_repository \
> co -r build26-branch gramene
>
> I also tried:
> $ cvs -d formaggio.cshl.org:/usr/local/cvs_repository \
> co -r build27-branch gramene
>
> But this CVS seems to be down, it returns this error message:
> 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 can download it from brebiou.cshl.edu:
> $ cvs -d :pserver:anonymous at brebiou.cshl.edu:/usr/local/cvs co gramene
> But it gives me release 21 of gramene.
>
> Where can I find this build27-branch of gramene project?
> Isn't it the same thing as what's found in gramene-27.0.0.tar.gz?
> If so, why are the instructions to download it from the CVS are 
> found in gramene-27.0.0.tar.gz?
>
> Thanks!

Jonathan,

We've just released version 28 today, so maybe you would have better 
luck just following those instructions?  Please let me know if you 
have any problems.

ky

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