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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