Re: [galaxy-dev] Galaxy 'environment' variables

24 May 2012

      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=%28me...). 
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