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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GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
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Mobil: +49 (0)151/ 14247360
Email: m.enders@german-seed-alliance.de
Firmensitz Köln
Amtsgericht Köln, HRB 73844
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Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org ] Im Auftrag von galaxy-dev-request@lists.galaxyproject.org
Gesendet: Donnerstag, 21. Dezember 2017 18:00
An: galaxy-dev@lists.galaxyproject.org
Betreff: galaxy-dev Digest, Vol 138, Issue 9
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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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>>
>>
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