Re: [galaxy-dev] error: flexbar dependency is not installed by the toolshed
Hello Rui, The problem here is that flexbar repository on the main Galaxy Tool Shed does not define a relationship between the flexbar tool contained within the repository and a recipe for installing the flexbar binary dependency. The flexbar tool config includes the following requirements tag set: requirements requirement type=binary version=2.4flexbar/requirement /requirements But there is no information about how to install the flexbar binary. The tool should have a a relationship to a recipt for installing the flexbar binary using the approach described here: https://wiki.galaxyproject.org/ToolsWitDependenciesInSeparateRepositories You can contact the tool author to report this problem. In the meantime, to use the tool, you'll have to install the flexbar dependency manually and make sure it can be found in the environment in which the tool is executed. Greg Von Kuster On May 19, 2014, at 10:07 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi Guys, I tried to install flexbar from toolshed, but upon running, error said it could not find it. I checked and found idtoolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4/id in the config file, but this path does not exist. Is it that I need to install the dependency on my own? I had the impression that toolshed will do it for me. Please correct me if I'm wrong. Thanks, Rui ___ 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/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] workflow delete cancelled but workflows are still deleted
Hello Evan, Thanks a bunch for the error report! I can confirm the problem and a hack to avoid it can be found here - https://github.com/jmchilton/galaxy-central/commit/306a86558a7ee7be1bc2d68cd939b16b5f1863d4.patch. I am going to give someone more familiar with the core GUI stuff a chance to fix the underlying problem before applying that hack to central though. I have created a Trello card to track progress on this issue here - https://trello.com/c/LWkgOJRV. Thanks, -John On Mon, May 19, 2014 at 2:57 PM, Evan Bollig boll0...@umn.edu wrote: I am working in the galaxy-dist stable branch. I select a workflow and select Delete. An alert pops up asking if I'm sure I want to do that. I press Cancel and the alert disappears, along with the workflow. This shouldn't happen. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.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/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy customized tool config file
Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool_shed_install.xml
Hey Evan, Out of curiosity, are you trying to update MSI's CLIA pipeline to utilize tool shed installed tools? (It sounds kind of like yes.) I don't think that file you mentioned exists in either place - is it a typo or maybe a configuration file with overridden location in universe_wsgi.ini? Reading between the lines, it sounds like you want Galaxy cloud images with completely fresh Galaxy instances but with preinstalled tools? There are many variants of the following approach that I think could work - but one approach is: Create a persistent directory (...or at least a directory that can be recreated when you launch a new VM) like: /mnt/gx_tools It should have the following contents: shed_tools/ (empty directory) shed_tool_conf.xml (contents like toolbox tool_path=/mnt/gx_tools/shed_tools/toolbox). dependencies/ (empty directory) Now create a throw away Galaxy instance and update its universe_wsgi.ini with the following properties: [app:main] tool_dependency_dir = /mnt/gx_tools/dependencies install_database_connection = sqlite:mnt/gx_tools/install_database.sqlite?isolation_level=IMMEDIATE tool_config_file = tool_conf.xml,/mnt/gx_tools/shed_tool_conf.xml Bootstrap and install tools. Throw away or wipe out Galaxy data and take a snapshot. Now just ensure new Galaxy VM instances starts with the above 3 properties set the same way. Hope this helps. -John On Tue, May 20, 2014 at 3:40 PM, Evan Bollig boll0...@umn.edu wrote: I want to setup a tool_shed_install.xml to roll out tools at first boot for Galaxy. 1) Is it possible to get Galaxy to generate this based on the tools currently installed from the tool shed? 2) Is it required to list every tool provided by each repository, or can I simply add the repository to the file and Galaxy will assume all tools are included? 3) The tool_shed_install.xml.sample file exists only in the galaxy-central#default branch. This should probably be included in the galaxy-dist#stable too. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.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/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool_shed_install.xml
Thanks John. I guess I'm looking at options enable_tool_shed_install and tool_shed_install_config_file that were added in rev 6398 and dropped in rev 6747 when the tool migration scripts were added. I don't know why they were dropped, but they would be immensely useful today. This is related to the CLIA pipeline, and a separate effort to simplify galaxy VM provisioning with puppet. From my perspective, copying in changes to that one file is significantly easier than grooming a mounted disk image. My end goal is dozens of independent galaxy instances running different tool chests. I might just merge the old code back in and submit a pull request, or I also see that a few scripted calls to scripts/api/install_tool_shed_repositories.py should also take care of it. Cheers, -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Tue, May 20, 2014 at 5:01 PM, John Chilton jmchil...@gmail.com wrote: Hey Evan, Out of curiosity, are you trying to update MSI's CLIA pipeline to utilize tool shed installed tools? (It sounds kind of like yes.) I don't think that file you mentioned exists in either place - is it a typo or maybe a configuration file with overridden location in universe_wsgi.ini? Reading between the lines, it sounds like you want Galaxy cloud images with completely fresh Galaxy instances but with preinstalled tools? There are many variants of the following approach that I think could work - but one approach is: Create a persistent directory (...or at least a directory that can be recreated when you launch a new VM) like: /mnt/gx_tools It should have the following contents: shed_tools/ (empty directory) shed_tool_conf.xml (contents like toolbox tool_path=/mnt/gx_tools/shed_tools/toolbox). dependencies/ (empty directory) Now create a throw away Galaxy instance and update its universe_wsgi.ini with the following properties: [app:main] tool_dependency_dir = /mnt/gx_tools/dependencies install_database_connection = sqlite:mnt/gx_tools/install_database.sqlite?isolation_level=IMMEDIATE tool_config_file = tool_conf.xml,/mnt/gx_tools/shed_tool_conf.xml Bootstrap and install tools. Throw away or wipe out Galaxy data and take a snapshot. Now just ensure new Galaxy VM instances starts with the above 3 properties set the same way. Hope this helps. -John On Tue, May 20, 2014 at 3:40 PM, Evan Bollig boll0...@umn.edu wrote: I want to setup a tool_shed_install.xml to roll out tools at first boot for Galaxy. 1) Is it possible to get Galaxy to generate this based on the tools currently installed from the tool shed? 2) Is it required to list every tool provided by each repository, or can I simply add the repository to the file and Galaxy will assume all tools are included? 3) The tool_shed_install.xml.sample file exists only in the galaxy-central#default branch. This should probably be included in the galaxy-dist#stable too. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.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/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] genotypeGVCFs in galaxy from GATK 3.0
Hi all, Is anyone working on (or has already created) wrappers for GATK 3.0? Specifically, I'm looking for a wrapper for genotypeGVCFs, but it seems like I would want all the GATK wrappers to be updated. Any help is highly appreciated! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
