To answer my own questions, apparently I missed the
outputs_to_working_directory setting in config/galaxy.ini.
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
> On 29 Dec 2015, at 14:04, Jorrit Boekel <jorrit.boe...@scilifelab.se> wrote:
> Dear all,
> I (finally) started transitioning our lab’s tools from using parallelism (the
> multi-splitter) towards collections. In the parallelism scenario, tools were
> run in their respective working dir, resulting from a chdir performed in
> extract_parts.sh. That was nice. But I see when using collections that there
> is a workdir around, but the tool is not actually run in it. I often need to
> symlink to change input file extensions and can’t imagine noone else does
> that, so I wondered if I was missing something. If I’m not, then here’s my
> two questions:
> - Is there an accepted place to symlink files in (and how do I pass the
> working dir in a tool XML)? I don’t want them in the files/ dir, looks bad,
> they’re not cleaned, etc etc.
> - Would it be a bad idea to make tools run inside a workdir, apart from
> possibly breaking backwards compatibility?
> Jorrit Boekel
> Proteomics systems developer
> BILS / Lehtiö lab
> Scilifelab Stockholm, Sweden
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