Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package
Hi Bjoern, Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_location_of_images_in_tool_configuration_files We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png so the variable is not being replaced by the value of the path...is this a known issue? Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 14:31 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-ability-to-change-the-tool/diff Cheers, Bjoern One extra detail I'm trying to find in the docs but haven't found yet: How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed? Example: -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a Tool test results container when viewing or managing the repository. Greg Von Kuster On Sep 12, 2013, at 7:23 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Ok, cool...I get the picture. One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicableI'm just thinking of scenarios where there is a bad update released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern Hi Greg, Fantastic, thanks for your detailed answer! I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ? Regards, Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new
Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package
Hi guys, We discovered that the problem is at our apache configuration side...working on it now... ;) Regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 12 september 2013 16:13 To: 'Bjoern Gruening' Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Bjoern, Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_location_of_images_in_tool_configuration_files We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png so the variable is not being replaced by the value of the path...is this a known issue? Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 14:31 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-ability-to-change-the-tool/diff Cheers, Bjoern One extra detail I'm trying to find in the docs but haven't found yet: How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed? Example: -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a Tool test results container when viewing or managing the repository. Greg Von Kuster On Sep 12, 2013, at 7:23 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Ok, cool...I get the picture. One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicableI'm just thinking of scenarios where there is a bad update released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern Hi Greg, Fantastic, thanks for your detailed answer! I am trying out some things and I noticed
