Hi Qi,
thank you very much for you contribution.
I will try to get your patch to the correct person during the upcoming
Galaxy Conference.
Cheers,
Bjoern
Am 13.06.2014 17:29, schrieb Qi, Chuyang:
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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