Proposed cd-hit tool dependency change in galaxy

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Proposed cd-hit tool dependency change in galaxy

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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Re: Proposed cd-hit tool dependency change in galaxy

Björn Grüning-3
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
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/