Sarah: I've had trouble before with invalid xml files (in your case test.xml) I don't see an obvious problem with your file, but I've never tried such a minimal file. Have a look at galaxy's log during startup to see if it tells you what it does not like about the file. Brad -- Brad Langhorst New England Biolabs langhorst@neb.com On 2/7/12 6:32 AM, "Sarah Maman" <sarah.maman@toulouse.inra.fr> wrote:
Hello,
I managed to add a new tool coded in bash but I am having some difficulty adding a tool coded in python.
Here are the contents of the test files: * Content of test.xml file in galaxy/galaxy-dist/tools/test/test.xml : <tool id="test" name="Test name"> <description>Test description</description> <command interpreter="python">test.py</command> </tool>
* Content of test.py file in galaxy/galaxy-dist/tools/test/test.py : #!/usr/bin/python
import os
for param in os.environ.keys(): print "%20s %s" % (param,os.environ[param])
* Content of tool_conf_xml file in galaxy/galaxy-dist/ : <?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="test/test.xml" /> <tool file="uploadFile/uploadFile.xml" /> <tool file="data_source/upload.xml"/> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />......
Could you, please, explain me why the new tool "test" isn't avalaible in Tools/Get Data windows (on the left, before uploadFile and upload tools ) ?
Thanks in advance, Sarah
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