Hi,

Thank for your answer, I copy you a part of the shell code

LOCAL_DIR= #{GALAXY_DIR}/galaxy-dist/tools/AnnotateGenes

R_DIR= #{R_PATH}/bin

echo "ChIP:" >$LOG

if [ -r $REG ]; then

  echo "1:  perl $LOCAL_DIR/geneAnnotation.pl -g
$LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -selG $REG -o
$OUTSTAT  -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE" >>
$LOGTMP

and a part of the xml

<tool id="annotateGenes" name="Annotation of genes with Chip-Seq peaks"
version="1.0">
  <description> </description>
  <command interpreter="bash"> #if $use_reg.use_reg_selector == "no" and
$use_control.use_control_selector == "no" #annotateGenes_wrapper.sh -f
$inputfile -y $log  -l $left -o $outputPNG -r $right -d $DownGene -h
$EnhLeft -u $stats -v $input_organism.version #elif
$use_reg.use_reg_selector == "no" and $use_control.use_control_selector
== "yes" # annotateGene_wrapper.sh -f $inputfile -y $log -c $controlfile
-x $statsControl -o $outputPNG  -l $left -r $right  -d $DownGene -h
$EnhLeft -u $stats -v $input_organism.version #elif
$use_reg.use_reg_selector == "yes" and $use_control.use_control_selector
== "no" # annotateGenes_wrapper.sh -y $log -f $inputfile -e $regfile  -l
$left -o $outputPNG -r $right  -d $DownGene -h $EnhLeft -u $stats -v
$input_organism.version #else # annotateGenes_wrapper.sh -f $inputfile
-c $controlfile -x $statsControl -l $left -y $log -o $outputPNG  -r $right
-d $DownGene  -h $EnhLeft -u $stats -v $input_organism.version -e $regfile
#end if


This tools are avaible in : http://nebula.curie.fr/

You can see that the variable LOCAL_DIR is the PATH of the tool so I would
like to know if it's possible to obtain this information without
hard-coded this?

Thank you for your answer.
Best Regards,

Fabien Mareuil

> Hello Fabien,
> I don't understand the issue - can you provide a sample tool config that
includes these hard-coded paths?  This initially sounds like an issue
with
> the tool configs, not the tool shed, but I may see the problem with your
clarification.
> Thanks,
> Greg Von Kuster
> On Jul 3, 2012, at 9:58 AM, Fabien Mareuil wrote:
>> Hi,
>> I have read the exchange betwen you and Florent Angly about "Problem with
>> new tool shed" and I have a problem with Nebula Tools:
>> http://nebula.curie.fr/.
>> At the Pasteur Institute, we have 4 galaxy instances and I would like
to
>> use a local tool shed instance for Nebula installation.
>> However, the nebula has tools with hard-coded path tool but I don't
want
>> hard-coded this so do you have a solution to add a thing like this
${tool.install_dir} in the xml?
>> Thank you for your answer.
>> Best Regards,
>> Fabien Mareuil
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