It is working WELL, and is very helpful !
Thanks a lot.
Fabrice
Scott Cain wrote:
Ah, right: I think the line that I quoted is from an older version of
CAS that had to use a modified version of the bash file. I forgot
that now all you have to do is supply the -H (I guess I was thinking
it used some form of magic :-)
Scott
On Sep 29, 2009, at 2:53 PM, Ed Lee wrote:
Hi Fabrice,
To be safe, you might want to run with the "-H" option (for recent
Apollo releases) to run in headless mode. As Scott mentioned,
the <chadodb> element in your "chado-adapter.xml" configuration
that has "<default-command-line-db>true</default-command-line-db>"
will be the one that is accessed when running from the command
line.
Cheers,
Ed
On Tue, 29 Sep 2009, Scott Cain wrote:
Hi Fabrice,
Can you already save to Chado via the GUI application? If so, the
command line stuff isn't too hard. The command I use in the
upload_game.pl cgi that is part of cas-utils
(http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/cas-utils/cgi-bin/upload_game.pl?revision=21941)
is this:
$apollo_path -f $fullfilename -i game -o chadoDB
where -f is the input file
-i is input type
-o is the output type
and Apollo will use the chado database marked as the "default for
command line" (or something like that) for loading the database.
If you don't have a reasonably recent version of Apollo, you might
also have to modify the bash script that launches Apollo to tell it
that it is launching in "headless" (ie, non-GUI) mode, but in the
recent release, that is handled cleanly by Apollo.
Scott
On Sep 29, 2009, at 12:23 PM, Fabrice Legeai wrote:
Hi,
I have a batch of game XML files (~300) I'd like to save directly
in my chadodb. As you can imagine, I'd rather use the command line
than the application. But, while I read carefully the help and
user guide about the command line options, I did not understand
how to proceed for saving directly gameXML in Chado. So a bit of
help is required.
thanks,
Fabrice Legeai
AphidBase, LepidoDB.
--
Fabrice Legeai
INRA UMR Bio3P IRISA Equipe Symbiose
IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 71 18
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
Fabrice Legeai
INRA UMR Bio3P IRISA Equipe Symbiose
IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 71 18
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apollo mailing list
[email protected]
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