Hi all,

When installing and testing the cd-hit tool from jjohnson from the main galaxy 
toolshed into my local instance of galaxy, I encountered a problem where galaxy 
cannot find the cd-hit program. 

The error was:
"/bin/sh: 1: cd-hit-est: not found"

As I debugged the problem, I found that there is an bug in the tool dependency. 
It installs the cd-hit programs but never moves the programs into the 
configurable galaxy install directory. This could cause many problems in the 
situation where users don't have cd-hit already installed on their computer and 
must depend on the tool dependency to run the tool.

I propose we add the following code to the tool dependency:

<action type="move_file">
           <source>cd-hit</source>
           <destination>$INSTALL_DIR</destination>
 </action>

<action type="move_file">
           <source>cd-hit-est</source>
           <destination>$INSTALL_DIR</destination>
 </action>

After I made these changes, I pushed the changes into a new repo on my local 
toolshed, I managed to successfully install cd-hit into a local and dev-test 
instance of galaxy and the cd-hit tool ran successfully. 

Thanks for your understanding,
Charles Qi

            


 
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