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 ${tool.install_dir} in the xml? Thank you for your answer. Best Regards, Fabien Mareuil ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Hello Fabien, This issue is indeed due to the tool design and is not related to the tool shed. I'm not primarily a tool developer, so I'm not the best person to help you with this issue. However, one recommendation would be to place your scripts and binaries that a specific tool wrapper uses in the same directory as the tool wrapper so that paths are not necessary. Some of the binaries may be more appropriately added to the environment path used by the user that starts up your Galaxy instance ( the R binaries are a good example ). This is the approach that the tools included in the Galaxy distribution use. The tool shed will not do anything special with tool wrapper that include hard-coded paths like this. The tool shed generally only makes sure that the tool loads properly in Galaxy. However, recent enhancements to the tool shed will handle tool dependencies that are properly defined in the tool config file within the <requirements> tag set. These new tool shed features will soon be documented in the tool shed wiki. Thanks, Greg Von Kuster On Jul 3, 2012, at 12:27 PM, Fabien Mareuil wrote:
Hi,
Thank for your answer, I copy you a part of the shell code
LOCAL_DIR= #{GALAXY_DIR}/galaxy-dist/tools/AnnotateGenes
R_DIR= #{R_PATH}/bin
echo "ChIP:" >$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 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/
participants (2)
-
Fabien Mareuil -
Greg Von Kuster