Tool_Path

Question: Tool_Path

6.4 years ago by

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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modified 6.4 years ago • written 6.4 years ago by Fabien Mareuil • 30

6.4 years ago by

Fabien Mareuil • 30

Fabien Mareuil • 30 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> #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 includes these hard-coded paths? This initially sounds like an issue with clarification. to want ${tool.install_dir} in the xml?

ADD COMMENT • link written 6.4 years ago by Fabien Mareuil • 30

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

ADD REPLY • link written 6.4 years ago by Greg Von Kuster ♦ 810

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