[galaxy-user] tool_path

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

Re: [galaxy-user] tool_path

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,

Re: [galaxy-user] tool_path

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

Re: [galaxy-user] tool_path

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