Problem with dependencies: Conda/freebayes - galaxy-dev

3 Jan 2018

      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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An: galaxy-dev@lists.galaxyproject.org
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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 luop0812@gmail.com
To: Hans-Rudolf Hotz hrh@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=ADoyw@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 hrh@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 <hrh@fmi.ch 
mailto:hrh@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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