[galaxy-dev] code tagset in tools
Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.glad...@unimelb.edu.au Web: http://www.vlsci.org.au ___ 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/
Re: [galaxy-dev] code tagset in tools
On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. Good question Simon. I am still using code for advanced parameter validation, e.g. https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml i.e. Validation before the job gets submitted to the cluster or run. If the code tag suddenly goes away, my tool will still work but would be a little less user friendly (some errors would only be spotted after the tool starts running). Peter ___ 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/
Re: [galaxy-dev] code tagset in tools
Hi Dan, Thanks for the reply and the suggestions. I think the data libraries would work much better than the get_microbial_data tool as then it would be more easily kept up to date. Cheers, Simon. On 30 April 2015 at 01:01, Daniel Blankenberg d...@bx.psu.edu wrote: The code tag won’t be going away any time soon, but in many cases there are other ways to do what this tag does, using the built-in dynamic options (in particular, currently for tab-delimited files), that are much preferred. So it is deprecated, and it should be used sparingly, but there are times when there isn’t a better way for tools to dynamically build their options without using a code file. In the case of the get microbial data tool, if it was working prior to 15.03, it should still be working, afaik we haven’t changed the handling of these recently (with the exception of not loading them inside of a ToolShed application instance). Its been a while since I’ve played with that specific tool (and we deprecated it ourselves and removed it from main), so I can’t confirm off-the-cuff whether it should still be working or not. If something really did break with respect to the code files, we should take a look though. I think using a Data Library is the perfect replacement for for the microbial import tool, and would cause less file duplication when used. But what exactly is no longer working? Thanks for using Galaxy, Dan On Apr 29, 2015, at 10:38 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. Good question Simon. I am still using code for advanced parameter validation, e.g. https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml i.e. Validation before the job gets submitted to the cluster or run. If the code tag suddenly goes away, my tool will still work but would be a little less user friendly (some errors would only be spotted after the tool starts running). Peter ___ 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/ -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.glad...@unimelb.edu.au Web: http://www.vlsci.org.au ___ 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/
Re: [galaxy-dev] code tagset in tools
The code tag won’t be going away any time soon, but in many cases there are other ways to do what this tag does, using the built-in dynamic options (in particular, currently for tab-delimited files), that are much preferred. So it is deprecated, and it should be used sparingly, but there are times when there isn’t a better way for tools to dynamically build their options without using a code file. In the case of the get microbial data tool, if it was working prior to 15.03, it should still be working, afaik we haven’t changed the handling of these recently (with the exception of not loading them inside of a ToolShed application instance). Its been a while since I’ve played with that specific tool (and we deprecated it ourselves and removed it from main), so I can’t confirm off-the-cuff whether it should still be working or not. If something really did break with respect to the code files, we should take a look though. I think using a Data Library is the perfect replacement for for the microbial import tool, and would cause less file duplication when used. But what exactly is no longer working? Thanks for using Galaxy, Dan On Apr 29, 2015, at 10:38 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. Good question Simon. I am still using code for advanced parameter validation, e.g. https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml i.e. Validation before the job gets submitted to the cluster or run. If the code tag suddenly goes away, my tool will still work but would be a little less user friendly (some errors would only be spotted after the tool starts running). Peter ___ 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/ ___ 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/
