[galaxy-dev] Keeping Galaxy up to date

Hello, I try to keep our Galaxy instance up to date. Very often, some tools disappear and other do not work anymore. This breaks some users workflows. I may miss something. Is there a best update pratice to keep a Galaxy instance and the tool-sheds fully functionnal ? Regards, Thomas --

Re: [galaxy-dev] Keeping Galaxy up to date

Hi Thomas, We had this topic at the GCC this year, especially within the Galaxy Admins BoF. The truth is (please correct me anyone if this is not the case anymore!) that you are touching an unresolved point. Keeping track of tools, settings etc. across the versions is not given. People have their

Re: [galaxy-dev] Keeping Galaxy up to date

Hi Sebastian, Thanks a lot for this detailed answer. I will think about a custom recipe and try to contribute to this topic. Thomas -- Thomas Bellembois, Network and System Administrator, IGFL (France) http://perso.ens-lyon.fr/thomas.bellembois - +33 4 26 73 13 67 (IGFL internal IT doc:

Re: [galaxy-dev] Keeping Galaxy up to date

Hello Thomas, After public debate on Trello, there have been a couple tools that have indeed disappeared completely but nearly all tools that have gone away have been migrated to the tool shed and can be recovered with the migration scripts that are included with each new release

[galaxy-dev] ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites'

Hi all, I'm wondering why my samtools_depad repository tests have failed, and since I have not changed this recently presume this is due to a Galaxy change or general TestToolShed problem not specific to my tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad Tests that failed

Re: [galaxy-dev] Output Excel file

Bjorn, that did the trick, thank you for the suggestion. Onwards! Patrick On Thu, Sep 4, 2014 at 2:41 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Patrick, a nice workaround is the following: Please create your file.xls file, but not in the path galaxy will provide, use a

Re: [galaxy-dev] Keeping Galaxy up to date

Hello John, I had forgotten that these migration scripts exist. It should work better now. :) Regards, Thomas -- Thomas Bellembois, Network and System Administrator, IGFL (France) http://perso.ens-lyon.fr/thomas.bellembois - +33 4 26 73 13 67 (IGFL internal IT doc:

[galaxy-dev] How to escape % characters in tool parameters?

Hi folks, I'm working on a tool that queries a database based on user input, where this user input is a text parameter. The wildcard for the database is the percent (%) character. The user input, which is ultimately translated into the query, should be able to contain a % character. For

Re: [galaxy-dev] How to escape % characters in tool parameters?

Funny - I just exchanged an e-mail with someone about this tool this morning, the Galaxy-P dbbuilder tool escapes exactly this santizing. Here is the relevant portion: param name=url value= type=text label=URL (http, ftp) sanitizer valid add value=%/

Re: [galaxy-dev] How to escape % characters in tool parameters?

Awesome! Thank you, John - I'd actually glanced at the sanitizer and wondered if it was what I needed, but having a working example makes all the difference! On Tue, Sep 9, 2014 at 7:26 PM, John Chilton jmchil...@gmail.com wrote: Funny - I just exchanged an e-mail with someone about this tool