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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
