[Gramene] SorghumCyc Feedback: upgrading Sorghumcyc 12.5 into 14

[Liya Ren]

Hi,

We haven't planned to update pathway-tools to v 14.0 now, but I  
upgrade the sorghumcyc on pathway-tools v 14.0 locally and have no  
problem so far. I have put the upgraded version  
sorghumcyc_v1_0_ptool_v14.tgz on our ftp site ftp://ftp.gramene.org/pub/gramene/pathways/sorghumcyc/ 
. Let me know if you still have a problem.


Liya

On Jun 27, 2010, at 3:12 PM, Sidibe bocs Stephanie wrote:

> Dear curators,
>
> As explained below, we have problems  upgrading from your SorghumCyc  
> database obtained with the PathwayTools version 12.5 into our  
> PathwayTools version 14.0.
> The ptools-support don't support the old pathway tools versions and  
> suggested to contact you  to obtained an upgraded version of your   
> work.
> Do you have the same problem? Could you please update SorghumCyc for  
> Pathway Tools version 14.0 ?
>
> Thank you very much for your help, best regards,
>
> Le 24/06/2010 21:43, Markus Krummenacker a écrit :
>>
>> Sidibe bocs Stephanie writes:
>>  > Dear all,
>>  >
>>  > We downloaded BioCyc / Pathway Tools Bundle Version 14.0.
>>  > For a first try, we want to browse and compare of already  
>> computed plant
>>  > data from our Web server connected to our database server.
>>  > So we also downloaded riceCyc, AraCyc, PoplarCyc, PlantCyc
>>  > http://www.plantcyc.org:1555/ARA/server.html?
>>  > http://www.gramene.org/pathway/
>>  >
>>  > Apparently there is a problem of version compatibility and the  
>> update
>>  > process does not work (see details below).
>>  > Should we work with the 12.5 Biocyc version ? if yes, where can we
>>  > download it ?
>>
>> Hi,
>>
>> Due to limited resources, we generally can't support such an old
>> Pathway Tools version, and it is no longer made available for  
>> download.
>>
>> But it is true that the upgrade of various plant-related PGDBs from
>> 12.5 to 14.0 caused several problems.  If I understand the situation,
>> PlantCyc and AraCyc have been successfully upgraded by now.  I don't
>> know when those new versions are made available for download.
>>
>> I suggest that you contact the staff at PlantCyc directly, and ask
>> them how you could obtain the upgraded versions that work with  
>> Pathway
>> Tools 14.0 .  This will save you a lot of problems.
>>
>>
>
> --------------------------------------------------------------------------------------------------
> I have problems with three biocyc databases : aracyc, plantcyc and  
> sorghumcyc.
> When I use pathwaytools in Web mode with this commande line
> $ ./pathway-tools -www
>
> This dialogue window open :
> The following PGDB(s) were built with, or last upgraded to Pathway  
> Tools version 12.5, and may be incompatible with the current Pathway  
> Tools version 14.0. Do you wish to upgrade now ?
> If you choose to upgrade now, you will need to specify a new version  
> number for each PGDB.
> If you choose not to upgrade, Pathway Tools will exit.
> Arabidopsis thaliana col (ARA)
> PlantCyc (PLANT)
> Sorghum biolor BTx623 (SORGHUM)
>
> I click on Upgrade Now, the window for changing the version number  
> for each PGDB opens and when I click on OK , this window close and I  
> have this error message :
>
> 244931920 bytes have been tenured, next gc will be global.
> See the documentation for variable EXCL:*GLOBAL-GC-BEHAVIOR* for  
> more information.
> Error: Invalid frame name RNA(N) in KB ARABASE:
>  Frame name "RNA(N)" contains the illegal character "("
> Error: KB ARABASE contains one or more frames whose names
> (unique identifiers) are syntactically invalid
> (contain illegal characters or exceed the allowed length).
>  [condition type: INVALID-FRAME-NAME]
>
> Restart actions (select using :continue):
> 0: Abort entirely from this (lisp) process.
>
> [changing package from "COMMON-LISP-USER" to "ECOCYC"]
> [Current process: Initial Lisp Listener]
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--
Liya Ren
ren at cshl.edu

www.gramene.org
Ware Lab
Cold Spring Harbor Laboratory

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