Possible to re-use toolconfig xml files outside Galaxy?
Hi, I have been looking into re-using the galaxy toolconfig xml files outside galaxy, for auto-generating wizards for command line tools, in an own little (eclipse based) software (For a short background, see [1]). I have come to realize though that the xml-files are not really independent, but (almost?) always is accompanied by a correpsonding .py file, which does more or less tricks, which seemingly makes it very hard to use the xml-files outside a galaxy/python environment at all. My questions: 1. Are the xml-files *always* accompanied by the .py file, or is that optional? 2. Would my idea be possible/reasonable at all? 3. Are there other more general tool config formats that I could use, since I'm not using galaxy atm? 4. Any other suggestions or ideas? Best Regards // Samuel [1]: The tool is built as a complement to some galaxy initiatives at the UPPMAX HPC Center in Uppsala. Specifically we need a light-weight way to configure batch scripts for the software installed at UPPMAX, of which bioinformatics tools are just a part. The galaxy toolconfig xml-format looked useful though, and seemed to enable us to have at least most of our bioinformatics tools (the category with most installed tools at UPPMAX) already configured. -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
Samual, as far as the xml goes. Yes it usually is accompanied by a py perl or bash script. However you could extract at least the user configurable options to gather input/output and setting parameters from the definition in the xml. In our case (we do use galaxy) we also have tools we use from commandline first and later provide it with a wrapper. Many tools in galaxy can be use like this but I guess many have more dependencies configured in for instance loc files in tool-data. My 2 ct Alex ________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Samuel Lampa [samuel.lampa@scilifelab.uu.se] Verzonden: woensdag 13 juli 2011 12:08 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Possible to re-use toolconfig xml files outside Galaxy? Hi, I have been looking into re-using the galaxy toolconfig xml files outside galaxy, for auto-generating wizards for command line tools, in an own little (eclipse based) software (For a short background, see [1]). I have come to realize though that the xml-files are not really independent, but (almost?) always is accompanied by a correpsonding .py file, which does more or less tricks, which seemingly makes it very hard to use the xml-files outside a galaxy/python environment at all. My questions: 1. Are the xml-files *always* accompanied by the .py file, or is that optional? 2. Would my idea be possible/reasonable at all? 3. Are there other more general tool config formats that I could use, since I'm not using galaxy atm? 4. Any other suggestions or ideas? Best Regards // Samuel [1]: The tool is built as a complement to some galaxy initiatives at the UPPMAX HPC Center in Uppsala. Specifically we need a light-weight way to configure batch scripts for the software installed at UPPMAX, of which bioinformatics tools are just a part. The galaxy toolconfig xml-format looked useful though, and seemed to enable us to have at least most of our bioinformatics tools (the category with most installed tools at UPPMAX) already configured. -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se ___________________________________________________________ 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/
Hi Alex, Much thanks for your input. On 07/13/2011 02:31 PM, Bossers, Alex wrote:
as far as the xml goes. Yes it usually is accompanied by a py perl or bash script. However you could extract at least the user configurable options to gather input/output and setting parameters from the definition in the xml.
Well, I'm just afraid that in too many occations, the input param flags and order for the accompanying (py/sh/perl) script might not be identical to the command line tool itself (or do the toolconfig generally avoid changing the flags and their order?). Best // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
participants (2)
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Bossers, Alex -
Samuel Lampa