To answer my own questions, apparently I missed the outputs_to_working_directory setting in config/galaxy.ini.
cheers, — Jorrit Boekel 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? > > cheers, > — > Jorrit Boekel > Proteomics systems developer > BILS / Lehtiö lab > Scilifelab Stockholm, Sweden > > > ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
