Hi Peter, I assume you are using a Galaxy instance within your development environment when developing new Galaxy tools so that you ultimately ensure your tool is functionally correct. Adding a local tool shed to your development environment will help you ensure that certain tool shed related processes (e.g., setting tool shed metadata, installing the repository into a local Galaxy, etc) are functionally correct.
With regard to proprietary datatypes (these are datatypes that are included in a tool shed repository), the process is simple if the datatypes are all subclassed from datatypes defined in the Galaxy framework. The emboss_datatypes are an example of this category, where the "type" attribute is something like "galaxy.datatypes.data:Text". You probably don't need to use a local tool shed to help in the development of tools that use this kind of proprietary datatype. The more complex category is when the proprietary datatypes subclass from proprietary classes defined in a code file in the repository. In this case, the class file's import statement definitions must be fully qualified. This is the category where using a local tool shed as a component of the development process may be beneficial as you can ensure the proprietary datatypes class file is written in such a way that the installation process into a local Galaxy instance is functionally correct. There is currently no way to define proprietary datatypes_conf.xml files in a configuration entry. Sorry for the long-winded answer - hopefully the context is helpful. Greg Von Kuster On Aug 23, 2012, at 10:11 AM, Peter Cock wrote: > Dear all, > > Until recently I'd not needed to define new datatypes while > developing tools for Galaxy - instead using (and sometimes > modifying) existing datatypes in situ. I have been manually > 'installing' my in-development tools by added their XML > files to tool_conf.xml - and this has worked fine to date. > > However, I would now like to experiment with defining or > modifying datatypes which would eventually be defined via > a datatypes_conf.xml file in a ToolShed entry. > > My impression from reading the latest wiki documentation > on http://wiki.g2.bx.psu.edu/Tool%20Shed is that I will have > to install my own local tool shed. > > Is there a simpler alternative? e.g. Can I add the new > datatypes_conf.xml file(s) to a configuration entry instead? > > Thanks, > > 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: > > http://lists.bx.psu.edu/ ___________________________________________________________ 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/