Hi Matthias,
sorry for answering so late!
Do you have any error message from the logs during installation?
What means it is not recognised by Galaxy?
Do you see the conda environment in /tool_deps/_conda/ ?
Is freebayes crashing?
Ciao,
Bjoern
Dear Galaxy Dev Mailing List,
We encountered a problem while installing freebayes and its via Tool
Shed.
Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19);
gawk (4.1.3) (all have the Current Installation Status "Installed
through Conda") but then failed on the last dependency "parallel".
(Status: "Not Installed")
The strange thing is: parallel was installed correctly. Its callable
from the command line, (e.g. parallel --help works fine) and
installed with the latest version. But it's not recognized by
Galaxy.
We are using the Galaxy - Docker image in Version 17.09.
Can you please assist us in resolving this?
Mit freundlichen Grüßen
Matthias Enders
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Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff:
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Today's Topics:
1. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)
----------------------------------------------------------------------
Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo
<luop0...@gmail.com> To: Hans-Rudolf Hotz <h...@fmi.ch> Cc: galaxy-dev
<galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Galaxy
v17.09 impersonation doesn't work Message-ID:
<CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ad...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hans-Rudolf,
I just started a brand new galaxy with the default internal database.
I did the minimal change to galaxy.ini so that I could use CAS
authentication. Still, impersonation failed.
Ping
On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <h...@fmi.ch>
wrote:
Hi Ping
Does it work with a fresh installation ( v17.09) staring with an
empty PostgrSQL database?
Hans-Rudolf
On 12/19/2017 03:41 PM, Ping Luo wrote:
Hans-Rudolf,
Yes, I have set the flag to be true
# Allow administrators to log in as other users (useful for
debugging) allow_user_impersonation = True
We use CAS authentication and our database is Postgresql. Our
current Galaxy is v15.07 and impersonation works well. I have
tried v16.10 before and impersonation didn't work either.
Thanks,
Ping
On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <h...@fmi.ch
<mailto:h...@fmi.ch>> wrote:
Hi Ping
The 'impersonate a user' function works for me with v17.09.
I assume, you have set: "allow_user_impersonation = True" in the
galaxy.ini file?
Do you encounter this problem, for the first time, i.e did it
work before using (v17.05 or earlier) and you only have the
issues after upgrading?
What database do you use?
Do you use external authentication?
Regards, Hans-Rudolf
On 12/18/2017 05:22 PM, Ping Luo wrote:
The impersonation feature in Galaxy v17.09 doesn't work as
expected.
After clicking the person to impersonate, the webpage shows "you
have now logged in as xxx, return to home page', where 'xxx' is
the name of the person I want to impersonate. So far so good. But
after I click home, and check the login information, the login
name is still myself.
Is there anything I missed in the configuration file?
Thanks,
Ping
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