Re: [galaxy-dev] error: flexbar dependency is not installed by the toolshed

2014-05-20 Thread Greg Von Kuster
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

Re: [galaxy-dev] workflow delete cancelled but workflows are still deleted

2014-05-20 Thread John Chilton
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

[galaxy-dev] Galaxy customized tool config file

2014-05-20 Thread Vipin TS
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

Re: [galaxy-dev] tool_shed_install.xml

2014-05-20 Thread John Chilton
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?

Re: [galaxy-dev] tool_shed_install.xml

2014-05-20 Thread Evan Bollig
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

[galaxy-dev] genotypeGVCFs in galaxy from GATK 3.0

2014-05-20 Thread Nikhil Joshi
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