Hi Luc,
The version used in our playbook actually references one of our pull requests
[1] and it looks like it references the most recent version. However, even the
most recent playbook on GitHub uses the incorrect URL. Something must have
changed since January.
In the interim you could try
Hi Sandra,
My initial hunch is that Ansible is trying to use root to create the
galaxy_privsep_user. Have you set galaxy_create_privsep_user to false in the
group_vars?
Cheers,
Keith
On Feb 15, 2021, at 12:21 AM, Sandra Maksimovic
mailto:sandra.maksimo...@mcri.edu.au>> wrote:
Hi there,
I don't
think this is appropriate to go into the GalaxySession and I don't see any
other "session-like" storage.
I'm sure to have more questions soon.
Cheers,
Keith
1. https://github.com/galaxyproject/galaxy/pull/9524
P.S. I will remember to squash my commits for the next PR ;)
> On Mar 12, 2020
eur we reverted back to Galaxy builtin auth even for internal
> users.
>
> In any case, if you got something working I'd be more than happy to
> test it.
>
> Youssef Ghorbal
> Institut Pasteur
> ---
>> On 7 Mar 2020, at 21:40, Keith Suderman wrote:
>
We are (finally) adding SAML authentication to our Galaxy instance so users can
authenticate with EduGain (EU) or InCommon (US). While doing some searching I
found an article that says, "Galaxy supports LDAP, SAML and now OIDC (see
https://galaxyproject.org/authnz/
Hi Pietro,
I suspect the package is broken. The anaconda.org server is available, but the
libgcc-ng file is not where the package expects it to be.
I followed your suggestion and it worked... sort of. At least it exposed
another error, actually the same problem but with numpy... So I applied
if set the `user_library_import_dir` to
> be the same as ftp and use `#user_library_import_dir_auto_creation: false`
>
> M.
>
> On Fri, Jan 25, 2019 at 4:58 PM Keith Suderman <mailto:suder...@cs.vassar.edu>> wrote:
> I have been creating directories for the users, but putting files in
f they are
> not there.
> Cicada
>
> ____
> From: galaxy-dev on behalf of
> Keith Suderman
> Sent: Friday, January 25, 2019 4:01 PM
> To: Galaxy Dev List
> Subject: [External] [galaxy-dev] Copying files to FTP upload directory
>
> Hello,
>
> I
Hello,
I am trying to (ab)use the FTP file upload functionality to get data from an
external service into Galaxy. From my reading of the docs I simply need to
configure the ftp_upload_dir and ftp_upload_site in my galaxy.ini (haven't
migrated to yaml yet) and Galaxy will expect to find
Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/
--
Keith Suderman
Research Associate
Depa
een
>window.setTimeout(function() {
>
> window.parent.$('#history-refresh-button').trigger('click');
>}, 3000);
>}
>});
>});
>});
>
>
> I hope it he
mended way to put data into the current
history via API calls?
2. How do I invoke the upload tool from JavaScript?
Thanks,
Keith
------
Keith Suderman
Research Associate
Department of Computer Science
Vassar College, Poughkeepsie NY
suder...@cs.vassar.edu
signature.asc
Descriptio
te.
> If you want to use this feature you need to indicate in your tool_conf.xml
> file which directory you would like to monitor.
> The syntax is like this:
>
>
>
> (The recursive="true" is not necessary if you want to monitor a flat
> directory).
>
> B
that goal.
- Keith
> On Feb 27, 2017, at 12:55 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:
>
> This all seems correct and I own you so many beers if you get this
> implemented! :)
>
> Am 27.02.2017 um 18:34 schrieb Keith Suderman:
>> Is anyone
I should
implement an external authenticator, something like
galaxy/auth/providers/saml.py and then some sort of magic to get a
config/auth_conf.xml working?
I just want to make sure I am heading down the correct path before investing
too much time.
- Keith
Keith Suderman
Research
Greetings,
I am trying to upgrade our Galaxy instance to the latest stable code from
master and now our instance won't start using my /etc/init.d/galaxy script.
That is:
> sudo service galaxy start
no longer works. It says it does (i.e. prints "[OK]"), but Galaxy isn't running
and nothing
if you want to
create a VIS.
Hope this helps,
Bjoern
Am 24.05.2015 um 02:45 schrieb Keith Suderman:
Greetings,
I am looking for information, tips, and pointers on writing a component for
visualizing text data in Galaxy. In particular I would like to use Brat
(http://brat.nlplab.org
Greetings,
I am looking for information, tips, and pointers on writing a component for
visualizing text data in Galaxy. In particular I would like to use Brat
(http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps.
The “Implementation Details” section on the
of 'convert.' in your datatypes_conf.xml at least if you are
not using the TS.
Hope this helps you a little bit more,
Bjoern
Thanks,
Keith Suderman
4. OAuth 2.0 / OpenID Connect:
I need to be able to fetch documents from data providers that require
an OAuth 2.0 access token. Currently, I
/converters/
And get rid of 'convert.' in your datatypes_conf.xml at least if you are
not using the TS.
Hope this helps you a little bit more,
Bjoern
Thanks,
Keith Suderman
4. OAuth 2.0 / OpenID Connect:
I need to be able to fetch documents from data providers that require
?
I guess you need to place your converters under
https://github.com/oanc/Galaxy/tree/master/lib/galaxy/datatypes/converters/
And get rid of 'convert.' in your datatypes_conf.xml at least if you are
not using the TS.
Hope this helps you a little bit more,
Bjoern
Thanks,
Keith Suderman
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