As feedback to the list
I have solved my problem below and a number of other issues I have had since
then with the "Toolfactory" available now from the Main Tool Shed (shameless
plug) that was created Ross Lazarus et al.
This tool allowed me to create a tool that was exactly what I wanted
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 wrote:
> Funny - I just exchanged an e-mail with someone about this tool this
> morning, the
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:
The full tool is on the tool shed.
https://tool
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 example
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: http://itdoc.igfl.ens-lyon.f
Bjorn, that did the trick, thank you for the suggestion.
Onwards!
Patrick
On Thu, Sep 4, 2014 at 2:41 PM, Björn Grüning
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 temporary path, for exampl
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
To
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
(https://wiki.g
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: http:/
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
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
--
Tho
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