Dear Jean-François,

But thanks for asking again, because now I had to look things up again, and now I found it. :-) Helping other people is apparently a strong drive to learn.

The only variables I have found, are following variables below (See alsohttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?highlight=%28metadata%29#A.3Ccommand.3E_tag_set). You can use them in the tool definition file as shown in example below.

$GALAXY_HOME : /home/galaxy/galaxy-dist
${GALAXY_DATA_INDEX_DIR}                      :$GALAXY_HOME/tool-data
$__new_file_path__ : universe_wsgi.ini's new_file_path --> temporary directory $__tool_data_path__ : tool_data_path value $__root_dir__ Top-level Galaxy source directory $__datatypes_config__ universe_wsgi.ini's datatypes_config value
$__user_id__                                   Email's numeric ID
$__user_email__                             User's email address
$__app__ (don't know about this one, seems to be deprecated)

<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?highlight=%28metadata%29#A.3Ccommand.3E_tag_set>
An example of what I like to do: I work with a 'configfile' to pass all parameters and galaxy settings to my tool/wrapper.

*Tool definition file:*
<tool  ....>
<command interpreter='perl'>
                          my_program.pl $configfile
</command>
<inputs>            ... configure here the inputs ... </inputs>
<configfiles>
<configfile name="$configfile">
        param1==$param1
        param2==$param2
        ...

        ##Galaxy Environment Variables
        tempdir==${__new_file_path__}*
*galaxyhome==${GALAXY_HOME}

</configfile>
</configfiles>
<outputs> ... </outputs>
<tests> </tests>
</tool>

*An my program 'my_program.pl' starts like:*

#!/usr/bin/perl
use strict;

#------------ PARSE GALAXY ARGUMENTS
# Get file with program parameters and Galaxy settings
#---------------------------------------------------------------------------#
my $configfile =$ARGV[0];


#------------- PARSE PARAMETERS
# Parse parameters from config file
#---------------------------------------------------------------------------##
my (%para);
open(CONFIG,"<$configfile");
while (<CONFIG>) {
    if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; }
}
close(CONFIG);

exit 0;

So now I have all parameters available in my program, in the hash %para, e.g. $para{'tempdir'}. Quick and easy!
I hope this is clear, if not, just ask.


Good luck with your implementation,

Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib



On 05/23/2012 08:26 PM, Jean-Francois Payotte wrote:
Dear Joachim,

I am interested at the exact same thing, such as finding a list of 'environment' variables in Galaxy.
Did you ever got your answer?

Best regards,
Jean-François



*[galaxy-dev] Galaxy 'environment' variables*

Joachim Jacob
Wed, 11 Apr 2012 08:18:46 -0700
Hello all,

Where can I find a list of 'environment' variables in Galaxy, such as:
$GALAXY_HOME
${GALAXY_DATA_INDEX_DIR}


More specifically, I am looking for the temporary directory setting of a user's Galaxy (as set in the universe_wsgi.ini).


Kind regards,
Joachim

--
Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
_http://www.bits.vib.be_ <http://www.bits.vib.be/>
@bitsatvib

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