From Jonathan.Arvisais at dnalandmarks.ca  Thu Oct  2 16:01:28 2008
From: Jonathan.Arvisais at dnalandmarks.ca (Jonathan Arvisais)
Date: Thu, 2 Oct 2008 16:01:28 -0400
Subject: [Gramene] gramene CVS and navigation bar
In-Reply-To: <D7E99FAF-ED5F-4392-866F-3AD48812C6E1@cshl.edu>
Message-ID: <OFC288605D.B1AE614F-ON852574D6.006DB733-852574D6.006E0084@notes.basf-corp.com>

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
Qu?bec, 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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From kclark at cshl.edu  Thu Oct  2 16:25:59 2008
From: kclark at cshl.edu (Ken Youens-Clark)
Date: Thu, 2 Oct 2008 15:25:59 -0500
Subject: [Gramene] gramene CVS and navigation bar
In-Reply-To: <OFC288605D.B1AE614F-ON852574D6.006DB733-852574D6.006E0084@notes.basf-corp.com>
References: <OFC288605D.B1AE614F-ON852574D6.006DB733-852574D6.006E0084@notes.basf-corp.com>
Message-ID: <168B6030-DEC5-4C65-A667-428E845E4537@cshl.edu>

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


From bluebear1211 at gmail.com  Tue Oct 21 23:30:09 2008
From: bluebear1211 at gmail.com (green tom)
Date: Wed, 22 Oct 2008 11:30:09 +0800
Subject: [Gramene] I can't get all the fast file for blastview
Message-ID: <e2c87f400810212030k5a2e187fs4961c9b46957096a@mail.gmail.com>

I am mirroring a  gramene web site and when i went to set up the blast
program , I can't find the all the fast file needed  by the ini files in the
ftp.gramene.org.    eg, I  can't  find " Aegilops.GRM23.est.fa "  needed by
 Aegilops.ini  in the  "/pub/gramene/release28/data/fasta/"  folder .    So,
where   can  I get   all fast file needed ?  How to set it correctly
 the  corresponding ini  files?
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From pj37 at cornell.edu  Fri Oct 24 13:42:04 2008
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 24 Oct 2008 10:42:04 -0700
Subject: [Gramene] Pathway database curator position at Gramene
Message-ID: <490208EC.4020804@cornell.edu>

Please circulate in your institutions and bulletin boards.

http://bivouac.cshl.edu/gramene-news/?p=44

A full time 3-year pathway database curator position at the Research 
Associate or Postdoctoral Associate level is available immediately in 
Dr. Pankaj Jaiswal?s group at the Department of Botany and Plant 
Pathology, Oregon State University, Corvallis, OR 
(http://www.science.oregonstate.edu/bpp/). This position is required to 
develop a comprehensive catalog of rice and other cereal plant metabolic 
pathways and enzymes. The project expands the coverage of metabolic 
pathways from Rice (http://gramene.org/pathway/) to all known pathways 
in major cereal plants such as for maize, sorghum and wheat. The curator 
will be responsible for development, curation and maintenance of the 
Pathways section on Gramene Database (http://www.gramene.org) in 
following ways.

i)    Develop novel methods on annotating the metabolic and regulatory 
pathway associations to the genomic and genetic datasets.
ii)    Research new plant metabolic pathways and enzymes in the 
scientific literature, and to evaluate, extract, organize, and enter 
that information to the database;
iii)    Development /improvement of new or existing standard procedures 
and operation rules on curation methods and to the general development 
of the database, such as data integration, web page enhancement, and 
data exchange with database namely the www.reactome.org.
iv)    Communicating with the research community to improve the quality 
of the data, to train them in using the database and related tools, and 
to support user requests.

The successful candidates will work with Gramene database team that 
includes highly trained PhD. level bioinformatics specialists and 
software developers. The person will also work with collaborator 
databases such as Rice Genome Annotation Project, MaizeGDB, GrainGenes, 
MetaCyc, PlantCyc, AraCyc, SolCyc, and a number of pioneering plant 
biochemists from around the world.

Qualified candidates should have a Ph.D. degree or equivalent in 
biochemistry, biological chemistry, metabolomics, or related field 
preferably in plants, but not necessarily. The successful candidate 
should also have a demonstrated ability for independent and critical 
thinking, excellent communication skills and enjoy teamwork. Experience 
with Lynux and Windows operating system, Perl, Java and HTML editing is 
desirable. Please send an email with a current CV/resume, and letter of 
interest to Pankaj Jaiswal (jaiswalp at oregonstate.edu). Oregon State 
University is an equal opportunity employer (EOE).



-- 
Pankaj Jaiswal
Assistant Professor
Dept. of Botany and Plant Pathology
3082 Cordley Hall
Oregon State University
Corvallis, OR, 97331-2902, USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
Web: www.gramene.org
      www.plantontology.org



From Jonathan.Arvisais at dnalandmarks.ca  Wed Oct 29 18:07:26 2008
From: Jonathan.Arvisais at dnalandmarks.ca (Jonathan Arvisais)
Date: Wed, 29 Oct 2008 18:07:26 -0400
Subject: [Gramene] CMap and Gramene navigation menu
Message-ID: <OFBB03D7F7.7BCEE3DD-ON852574F1.00768ACE-852574F1.007988FB@notes.basf-corp.com>

Hi,

Our local installation of Gramene is progressing well. The ensembl genome 
browser is working well. Thanks for your help.

I had to do this to get CMap to work:
- in the folder '/usr/local/ensembl/', create a symbolic link named 
'cgi-perl' that links to the folder '/usr/local/gramene/cgi-perl/'
- changed the '/db/' links to '/cgi-perl/' in the file 
'/usr/local/gramene/html/cmap/index.html'

Is there a problem with the '/db' alias configured in the file 
'/usr/local/gramene/conf/httpd.conf' ?
push @Alias ,    ['/db'         => "$ServerRoot/cgi-perl"],
push @ScriptAlias, ['/db' => "$ServerRoot/cgi-perl/"];

With this fix, CMap now works but I can't get the Gramene navigation menu 
to display.
The 'page_object Gramene::Page' statement is already present in the file 
'/usr/local/gramene/conf/cmap.conf/gramene-build28.conf' provided by 
Gramene.

Thanks!

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