URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:*143* in __call__ body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*184* in decorator
Hello Franco, It's impossible to help you with this issue and the issues you sent in your previous messages unless you provide more information. What version of Galaxy are you running? From what tool shed are you installing repositories. What repository are you installing? What are the precise steps you took to produce the behavior? Keep in mind that the Galaxy test tool shed tracks the galaxy-central repository on bitbucket while the Galaxy main tool shed tracks the galaxy-dist repository on bitbucket. Greg Von Kuster On Dec 2, 2012, at 11:36 PM, Franco Caramia wrote:
Hi Greg, Our Galaxy version is galaxy-dist 7712:e6444e7a1685 . The tool is ³contra² from this repo: http://fcaramia@toolshed.g2.bx.psu.edu/repos/fcaramia/contra I own the repo and uploaded the tool_dependencies file Then the following steps: Installing the tool from toolshed: Success Installing tool dependencies: Failed Deleting tool: Success Re-installing tool: Failed Thanks, Franco On 4/12/12 12:40 AM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
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Hi Franco, You're running a fairly old version of Galaxy - the main Galaxy tool shed tracks the galaxy-dist repository on bitbucket. You should upgrade to the latest dist release which went out today - the change set is 8286:f364d992270c. We'll take a look at reproducing this behavior first thing tomorrow with the dist revision to ensure there are no problems using your steps below. If we discover any issues we'll let you know. Thanks for the additional information. Greg Von Kuster On Dec 3, 2012, at 9:21 PM, Franco Caramia wrote:
Hello Franco, The tool dependency installation fails due to BEDTools.v2.17.0.tar.gz extracting into a directory named bedtools-2.17.0, rather than BEDTools.v2.17.0. Also, you following tag is not optimal since it assumes a specific os platform. <action type="shell_command">cp bin/* $INSTALL_DIR/bin</action> You'll need to change your tool_dependency.xml definition to use the "target_file" option, and correct the above tag with something like the following: <?xml version="1.0"?> <tool_dependency> <package name="bedtools" version="2.17.0"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz">http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> <action type="shell_command">make clean</action> <action type="shell_command">make all</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools </readme> </package> </tool_dependency> Greg Von Kuster On Dec 3, 2012, at 9:21 PM, Franco Caramia wrote:
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Greg Von Kuster