Hello Fabien,

This issue is indeed due to the tool design and is not related to the tool 
shed.  I'm not primarily a tool developer, so I'm not the best person to help 
you with this issue.  

However, one recommendation would be to place your scripts and binaries that a 
specific tool wrapper uses in the same directory as the tool wrapper so that 
paths are not necessary.  Some of the binaries may be more appropriately added 
to the environment path used by the user that starts up your Galaxy instance ( 
the R binaries are a good example ).  This is the approach that the tools 
included in the Galaxy distribution use.

The tool shed will not do anything special with tool wrapper that include 
hard-coded paths like this.  The tool shed generally only makes sure that the 
tool loads properly in Galaxy.  However, recent enhancements to the tool shed 
will handle tool dependencies that are properly defined in the tool config file 
within the <requirements> tag set.  These new tool shed features will soon be 
documented in the tool shed wiki.

Thanks,

Greg Von Kuster

On Jul 3, 2012, at 12:27 PM, Fabien Mareuil wrote:

> 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
>>> ___________________________________________________________
>>> The Galaxy User list should be used for the discussion of
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> 
> 
> 
> 


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