Re: [galaxy-dev] Making symlinks in "command" section of tool XML

[John Chilton]

At first glace I think the problem is that when you use the
``interpreter`` tag Galaxy has really broken logic for modifying the
command line to use that. ln works just like cp and mv. Those too
would be broken for this tool because of the interpreter attribute I
think. For this reason ``interpreter`` has been deprecated
(https://docs.galaxyproject.org/en/latest/dev/schema.html#id3) and
should not be used.

I would drop the interpreter="bash" stuff and just where ever your
script (lets say script_name.bash) appears in the command replace the
reference to script_name.bash with:

bash $__tool_directory__/script_name.bash

I think this will work a lot better for you. Let me know if it does not.

-John


On Thu, Jan 19, 2017 at 10:05 AM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
> Dear Developers
>
> I'm currently looking at develop a tool for a local pipeline, and want to
> make symlinks as part of the script in the "command" section of the tool XML
> - something like e.g.
>
>   <command interpreter="bash"><![CDATA[
>   ## Create links to input FASTQs and Final_names.txt file
>   #for $fq_pair in $fastq_pairs
>     ln -s "${fq_pair.fastq_r1}" &&
>     ...
>   #end for
>   ...
>
> But when I try running the tool I get a failure with the message:
>
> Fatal error: Exit code 127 ()
> bash: /PATH/TO/TOOL/DIR/ln: No such file or directory
>
> (NB I've snipped out the real path above, but essentially it's the directory
> where the tool XML is installed.)
>
> I know that it's permissible to use 'cp' and 'mv' in this context, so is
> 'ln' treated differently? Is there an alternative way to make symlinks in
> the command?
>
> Thanks for your help!
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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