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

[Peter Briggs]

Hello John

Thanks for the prompt reply, and the heads-up re the deprecation of the 
"interpreter" attribute. It looks removing this attribute from the 
"command" tag fixes the linking problem, as you say.

I'll try the new idiom referencing $__tool_directory__ and let you know 
if I have any issues.

Thanks for your help!

Best wishes

Peter

On 19/01/17 15:38, John Chilton wrote:
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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--
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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