Hi Keith,
> Hi Björn, > > Have you pushed the new version to the Docker Hub? When I run the > galaxy-stable image with the -e BARE=true option I still get a Galaxy > instance with the default tools. Yes it is, but you need the :dev version, aka: docker run -i -t -p 8080:80 bgruening/galaxy-stable:dev (hope it works, I'm currently not on my PC) > Also, does this really give me a “bare” Galaxy instance, or just a > Galaxy instance with an empty tool_conf.xml file? It only deactivates the tools in tool_conf.xml files. Is this is problem? These tools do not have any dependencies other than python and disc space should not be a problem as these are only a bunch of XML files. The my comments inline. >> >> Am 31.03.2016 um 22:17 schrieb Suderman Keith: >>> Dear Galaxy Team, >>> >>> Two questions. >>> >>> 1) Is there a bare-bones version of Galaxy available somewhere? >>> That is, Galaxy with no tools pre-installed? We are creating >>> Ansible play books for configuring Docker/Galaxy instances with >>> our NLP tools installed. Currently we are using a fork of the >>> Galaxy project with the bio tools removed, but this is less than >>> ideal when we try to update to new versions of Galaxy. Can you explain what you delete? I do really support this idea as we are also developing cheminformatics or imaging flavours. >>> Alternatively, does anyone have an automated process to delete >>> unwanted tools that we could run immediately after cloning the >>> main Galaxy repo? I don't think so you are pioneering here! But I think the gain of this step is currently not much, isn't it? What are your concerns? Disc-space? As a fist shoot I would try to hide genomic-specifc stuff from users. In a long run we can talk about this with the Galaxy team, isn't it. I know there is already a consensus of getting tools into the TS and have as less as possible tools in Galaxy by default. If you look 3 years back, Galaxy was full of tools, nowadays it's more or less text manipulation tools without dependencies. So plain XML files with a few scripts. >>> 2) Is is possible to either a) modify the existing upload tool, >>> or b) implement a new upload tool? Several options in the upload >>> tool do not make sense in our domain (e.g. selecting a genome) >>> and we would also like to do some post-processing to files after >>> they have been uploaded. I've looked at the code for the >>> existing upload tool and it seems quite tightly coupled to the >>> Galaxy code base. Yes it is, actually you need to have the upload tool, otherwise many things do not work. I would like to go with a)! That is put big #if #else conditions in the JS and Galaxy code to display genomic-specific content ... we could have a galaxy.ini config to trigger this #if. I do think we have a good chance to get this accepted. Second step, and this will take for careful thoughts, is a plugin mechanism for post-upload modifications. The currently upload tool has some kind of these functionality, for example the "Space-To-Tab" converter. Ideally exposing tools (even from the TS)? >>> I was hoping the "Downgrade upload tool" >>> thread from a few weeks ago was going to help, but unfortunately >>> for me (and good for the user) they found a solution that didn't >>> involve installing a new upload tool. Let's try to stay as upstream as possible. upload.xml is so tightly integrated in Galaxy that it is better to get code upstream I assume. And I know Galaxy devs like the idea of being less genomic centric and more a general framework. It's just that no one had time for this until know. >>> However, could I follow the approach suggested in that thread? >>> I.E. go back in time and find an old upload.[py | xml] and use >>> that as a starting point for my own custom upload tool? How far >>> back in time would I have to go to find an upload.py that was a >>> standalone tool? I think this will cause more trouble ... :( Let me know what you decide I will try to help you as much as I can. Cheers, Bjoern >>> Cheers, Keith >>> >>> ------------------------------ Research Associate Department of >>> Computer Science Vassar College Poughkeepsie, NY >>> >>> >>> >>> ___________________________________________________________ >>> 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/ >>> > > ------------------------------ Research Associate Department of > Computer Science Vassar College Poughkeepsie, NY > ___________________________________________________________ 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/
