Problem with dependencies: Conda/freebayes

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Problem with dependencies: Conda/freebayes

Matthias Enders
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
-----------------------------------------------------------------------


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

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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 <[hidden email]>
To: Hans-Rudolf Hotz <[hidden email]>
Cc: galaxy-dev <[hidden email]>
Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work
Message-ID:
        <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=[hidden email]>
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 <[hidden email]> 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 <[hidden email]
>> <mailto:[hidden email]>> 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
>>
>>
>>         ___________________________________________________________
>>         Please keep all replies on the list by using "reply all"
>>         in your mail client.  To manage your subscriptions to this
>>         and other Galaxy lists, please use the interface at:
>>         https://lists.galaxyproject.org/ 
>> <https://lists.galaxyproject.o rg/>
>>
>>         To search Galaxy mailing lists use the unified search at:
>>         http://galaxyproject.org/search/ 
>> <http://galaxyproject.org/sear ch/>
>>
>>
>>
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Re: Problem with dependencies: Conda/freebayes

Björn Grüning-3
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
> -----------------------------------------------------------------------
>
>
>
> GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg
> Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: +
> 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360
>
> Email: [hidden email]
>
> Firmensitz Köln Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht----- Von: galaxy-dev
> [mailto:[hidden email]] Im Auftrag von
> [hidden email] Gesendet: Donnerstag, 21.
> Dezember 2017 18:00 An: [hidden email] Betreff:
> galaxy-dev Digest, Vol 138, Issue 9
>
> Send galaxy-dev mailing list submissions to
> [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email,
> send a message with subject or body 'help' to
> [hidden email]
>
> You can reach the person managing the list at
> [hidden email]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of galaxy-dev digest..."
>
>
> HEY!  This is important!  If you reply to a thread in a digest,
> please 1. Change the subject of your response from "Galaxy-dev Digest
> Vol ..." to the original subject for the thread. 2. Strip out
> everything else in the digest that is not part of the thread you are
> responding to.
>
> Why? 1. This will keep the subject meaningful.  People will have some
> idea from the subject line if they should read it or not. 2. Not
> doing this greatly increases the number of emails that match search
> queries, but that aren't actually informative.
>
> 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
> <[hidden email]> To: Hans-Rudolf Hotz <[hidden email]> Cc: galaxy-dev
> <[hidden email]> Subject: Re: [galaxy-dev] Galaxy
> v17.09 impersonation doesn't work Message-ID:
> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=[hidden email]>
> 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 <[hidden email]>
> 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 <[hidden email]
>>> <mailto:[hidden email]>> 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
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all" in your
>>> mail client.  To manage your subscriptions to this and other
>>> Galaxy lists, please use the interface at:
>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.o
>>> rg/>
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/ <http://galaxyproject.org/sear
>>> ch/>
>>>
>>>
>>>
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> scrubbed... URL:
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>
>  ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________ galaxy-dev mailing
> list [hidden email]
> https://lists.galaxyproject.org/listinfo/galaxy-dev
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
> ------------------------------
>
> End of galaxy-dev Digest, Vol 138, Issue 9
> ******************************************
> ___________________________________________________________ Please
> keep all replies on the list by using "reply all" in your mail
> client.  To manage your subscriptions to this and other 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/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: Problem with dependencies: Conda/freebayes

Devon Ryan
This is presumably the same question elsewhere:
https://biostar.usegalaxy.org/p/26197/
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Jan 11, 2018 at 9:44 AM, Björn Grüning
<[hidden email]> wrote:

> 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
>> -----------------------------------------------------------------------
>>
>>
>>
>> GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg
>> Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: +
>> 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360
>>
>> Email: [hidden email]
>>
>> Firmensitz Köln Amtsgericht Köln, HRB 73844
>>
>> -----Ursprüngliche Nachricht----- Von: galaxy-dev
>> [mailto:[hidden email]] Im Auftrag von
>> [hidden email] Gesendet: Donnerstag, 21.
>> Dezember 2017 18:00 An: [hidden email] Betreff:
>> galaxy-dev Digest, Vol 138, Issue 9
>>
>> Send galaxy-dev mailing list submissions to
>> [hidden email]
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email,
>> send a message with subject or body 'help' to
>> [hidden email]
>>
>> You can reach the person managing the list at
>> [hidden email]
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of galaxy-dev digest..."
>>
>>
>> HEY!  This is important!  If you reply to a thread in a digest,
>> please 1. Change the subject of your response from "Galaxy-dev Digest
>> Vol ..." to the original subject for the thread. 2. Strip out
>> everything else in the digest that is not part of the thread you are
>> responding to.
>>
>> Why? 1. This will keep the subject meaningful.  People will have some
>> idea from the subject line if they should read it or not. 2. Not
>> doing this greatly increases the number of emails that match search
>> queries, but that aren't actually informative.
>>
>> 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
>> <[hidden email]> To: Hans-Rudolf Hotz <[hidden email]> Cc: galaxy-dev
>> <[hidden email]> Subject: Re: [galaxy-dev] Galaxy
>> v17.09 impersonation doesn't work Message-ID:
>> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=[hidden email]>
>> 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 <[hidden email]>
>> 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 <[hidden email]
>>>> <mailto:[hidden email]>> 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
>>>>
>>>>
>>>> ___________________________________________________________ Please keep
>>>> all replies on the list by using "reply all" in your
>>>> mail client.  To manage your subscriptions to this and other
>>>> Galaxy lists, please use the interface at:
>>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.o
>>>> rg/>
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/ <http://galaxyproject.org/sear
>>>> ch/>
>>>>
>>>>
>>>>
>> -------------- next part -------------- An HTML attachment was
>> scrubbed... URL:
>>
>> <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171220/a562a405/attachment-0001.html>
>>
>>  ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________ galaxy-dev mailing
>> list [hidden email]
>> https://lists.galaxyproject.org/listinfo/galaxy-dev
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>> ------------------------------
>>
>> End of galaxy-dev Digest, Vol 138, Issue 9
>> ******************************************
>> ___________________________________________________________ Please
>> keep all replies on the list by using "reply all" in your mail
>> client.  To manage your subscriptions to this and other 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/
>>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other 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/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Problem with dependencies: Conda/freebayes

Jennifer Hillman-Jackson
In reply to this post by Matthias Enders
Hello,

Did the suggested help from Biostars help? https://biostar.usegalaxy.org/p/26197/

Thanks!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support

On Wed, Jan 3, 2018 at 6:01 AM, Matthias Enders <[hidden email]> wrote:
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
-----------------------------------------------------------------------


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: galaxy-dev [mailto:[hidden email]] Im Auftrag von [hidden email]
Gesendet: Donnerstag, 21. Dezember 2017 18:00
An: [hidden email]
Betreff: galaxy-dev Digest, Vol 138, Issue 9

Send galaxy-dev mailing list submissions to
        [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
        https://lists.galaxyproject.org/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
        [hidden email]

You can reach the person managing the list at
        [hidden email]

When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..."


HEY!  This is important!  If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you are responding to.

Why?
1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.

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 <[hidden email]>
To: Hans-Rudolf Hotz <[hidden email]>
Cc: galaxy-dev <[hidden email]>
Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work
Message-ID:
        <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=[hidden email]>
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 <[hidden email]> 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 <[hidden email]
>> <mailto:[hidden email]>> 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
>>
>>
>>         ___________________________________________________________
>>         Please keep all replies on the list by using "reply all"
>>         in your mail client.  To manage your subscriptions to this
>>         and other Galaxy lists, please use the interface at:
>>         https://lists.galaxyproject.org/
>> <https://lists.galaxyproject.o rg/>
>>
>>         To search Galaxy mailing lists use the unified search at:
>>         http://galaxyproject.org/search/
>> <http://galaxyproject.org/sear ch/>
>>
>>
>>
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Problem with dependencies: Conda/freebayes

Matthias Enders
In reply to this post by Matthias Enders
Following the suggestion from Devon Ryan @ https://biostar.usegalaxy.org/p/26197/
Our IT-people re-do the installation several times, until it works out.

So it works on occasion..

Mit freundlichen Grüßen

Matthias Enders
-----------------------------------------------------------------------


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: galaxy-dev [mailto:[hidden email]] Im Auftrag von [hidden email]
Gesendet: Donnerstag, 11. Januar 2018 18:00
An: [hidden email]
Betreff: galaxy-dev Digest, Vol 139, Issue 4
Priorität: Hoch

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2. Strip out everything else in the digest that is not part of the thread you are responding to.

Why?
1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.

Today's Topics:

   1. Re: Problem with dependencies: Conda/freebayes (Björn Grüning)
   2. Re: Problem with dependencies: Conda/freebayes (Devon Ryan)
   3. Re: Problems installing conda dependencies for seq2hla tool
      (Peter Briggs)
   4. Re: Problem with dependencies: Conda/freebayes
      (Jennifer Hillman-Jackson)


----------------------------------------------------------------------

Message: 1
Date: Thu, 11 Jan 2018 09:44:10 +0100
From: Björn Grüning <[hidden email]>
To: Matthias Enders <[hidden email]>,
        "[hidden email]"
        <[hidden email]>
Cc: Fabian Kaiser <[hidden email]>
Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=utf-8; format=flowed

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
> ----------------------------------------------------------------------
> -
>
>
>
> GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg
> Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: +
> 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360
>
> Email: [hidden email]
>
> Firmensitz Köln Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht----- Von: galaxy-dev
> [mailto:[hidden email]] Im Auftrag von
> [hidden email] Gesendet: Donnerstag, 21.
> Dezember 2017 18:00 An: [hidden email] Betreff:
> galaxy-dev Digest, Vol 138, Issue 9
>
> Send galaxy-dev mailing list submissions to
> [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email,
> send a message with subject or body 'help' to
> [hidden email]
>
> You can reach the person managing the list at
> [hidden email]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of galaxy-dev digest..."
>
>
> HEY!  This is important!  If you reply to a thread in a digest, please
> 1. Change the subject of your response from "Galaxy-dev Digest Vol
> ..." to the original subject for the thread. 2. Strip out everything
> else in the digest that is not part of the thread you are responding
> to.
>
> Why? 1. This will keep the subject meaningful.  People will have some
> idea from the subject line if they should read it or not. 2. Not doing
> this greatly increases the number of emails that match search queries,
> but that aren't actually informative.
>
> 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
> <[hidden email]> To: Hans-Rudolf Hotz <[hidden email]> Cc: galaxy-dev
> <[hidden email]> Subject: Re: [galaxy-dev] Galaxy
> v17.09 impersonation doesn't work Message-ID:
> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=[hidden email]>
> 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 <[hidden email]>
> 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 <[hidden email]
>>> <mailto:[hidden email]>> 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
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all" in your
>>> mail client.  To manage your subscriptions to this and other Galaxy
>>> lists, please use the interface at:
>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.o rg/>
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/ <http://galaxyproject.org/sear ch/>
>>>
>>>
>>>
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>
> Subject: Digest Footer
>
> _______________________________________________ galaxy-dev mailing
> list [hidden email]
> https://lists.galaxyproject.org/listinfo/galaxy-dev
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
> ------------------------------
>
> End of galaxy-dev Digest, Vol 138, Issue 9
> ******************************************
> ___________________________________________________________ Please
> keep all replies on the list by using "reply all" in your mail client.  
> To manage your subscriptions to this and other 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/
>


------------------------------

Message: 2
Date: Thu, 11 Jan 2018 09:47:42 +0100
From: Devon Ryan <[hidden email]>
To: Björn Grüning <[hidden email]>
Cc: Fabian Kaiser <[hidden email]>,
        "[hidden email]"
        <[hidden email]>, Matthias Enders
        <[hidden email]>
Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes
Message-ID:
        <CADus9os+Adb=[hidden email]>
Content-Type: text/plain; charset="UTF-8"

This is presumably the same question elsewhere:
https://biostar.usegalaxy.org/p/26197/
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51
79108 Freiburg
Germany


On Thu, Jan 11, 2018 at 9:44 AM, Björn Grüning <[hidden email]> wrote:

> 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
>> ---------------------------------------------------------------------
>> --
>>
>>
>>
>> GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg
>> Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: +
>> 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360
>>
>> Email: [hidden email]
>>
>> Firmensitz Köln Amtsgericht Köln, HRB 73844
>>
>> -----Ursprüngliche Nachricht----- Von: galaxy-dev
>> [mailto:[hidden email]] Im Auftrag von
>> [hidden email] Gesendet: Donnerstag, 21.
>> Dezember 2017 18:00 An: [hidden email] Betreff:
>> galaxy-dev Digest, Vol 138, Issue 9
>>
>> Send galaxy-dev mailing list submissions to
>> [hidden email]
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email,
>> send a message with subject or body 'help' to
>> [hidden email]
>>
>> You can reach the person managing the list at
>> [hidden email]
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of galaxy-dev digest..."
>>
>>
>> HEY!  This is important!  If you reply to a thread in a digest,
>> please 1. Change the subject of your response from "Galaxy-dev Digest
>> Vol ..." to the original subject for the thread. 2. Strip out
>> everything else in the digest that is not part of the thread you are
>> responding to.
>>
>> Why? 1. This will keep the subject meaningful.  People will have some
>> idea from the subject line if they should read it or not. 2. Not
>> doing this greatly increases the number of emails that match search
>> queries, but that aren't actually informative.
>>
>> 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
>> <[hidden email]> To: Hans-Rudolf Hotz <[hidden email]> Cc: galaxy-dev
>> <[hidden email]> Subject: Re: [galaxy-dev] Galaxy
>> v17.09 impersonation doesn't work Message-ID:
>> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=[hidden email]>
>> 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 <[hidden email]>
>> 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 <[hidden email]
>>>> <mailto:[hidden email]>> 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
>>>>
>>>>
>>>> ___________________________________________________________ Please
>>>> keep all replies on the list by using "reply all" in your mail
>>>> client.  To manage your subscriptions to this and other Galaxy
>>>> lists, please use the interface at:
>>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.o 
>>>> rg/>
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/ <http://galaxyproject.org/sear 
>>>> ch/>
>>>>
>>>>
>>>>
>> -------------- next part -------------- An HTML attachment was
>> scrubbed... URL:
>>
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>> 71220/a562a405/attachment-0001.html>
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>>
>> Subject: Digest Footer
>>
>> _______________________________________________ galaxy-dev mailing
>> list [hidden email]
>> https://lists.galaxyproject.org/listinfo/galaxy-dev
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>> ------------------------------
>>
>> End of galaxy-dev Digest, Vol 138, Issue 9
>> ******************************************
>> ___________________________________________________________ Please
>> keep all replies on the list by using "reply all" in your mail
>> client.  To manage your subscriptions to this and other 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/
>>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
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------------------------------

Message: 3
Date: Thu, 11 Jan 2018 10:19:46 +0000
From: Peter Briggs <[hidden email]>
To: "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] Problems installing conda dependencies for
        seq2hla tool
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Just to follow up on my own question, in case it's helpful to anyone else:

Re the specific problem with not being able to install the seq2HLA 2.2 dependency via conda: in the end I build my own version and made it available to Galaxy as "Galaxy package" (https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html#galaxy-packages-dependency-resolver), which seemed to work okay.

Re updating to conda 4.3.24: after the update this gave me problems with at least one dependency, due to the "--offline bug" described here:
https://github.com/galaxyproject/galaxy/issues/5187

I applied Norbert Eichner's fix in PR #5233 (https://github.com/galaxyproject/galaxy/pull/5233) and reinstalled the conda dependency via "Manage Tool Dependencies" in the "Admin" interface, which seemed to fix that problem. It's not clear to me yet whether other conda dependencies might need to be reinstalled, or if applying the patch is sufficient.

Best wishes

Peter


--
Peter Briggs [hidden email] Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


________________________________________
From: galaxy-dev [[hidden email]] on behalf of Peter Briggs [[hidden email]]
Sent: Friday, January 05, 2018 12:06 PM
To: [hidden email]
Subject: [galaxy-dev] Problems installing conda dependencies for seq2hla tool

Dear Devs

I've been having problems installing the jjohnson/seq2hla tool from the toolshed on our production instance (running release_17.09).

Specifically Galaxy has been unable to successfully install the seq2HLA 2.2 dependency via conda. However it seems to work fine when installing into a clean local instance.

Initially the problem seemed to be that our version of conda was too old (we had 4.2.13), so while the __seq2HLA@2.2 env was being created, the 'seq2hla' package couldn't be installed into it (so Galaxy thought that the requirement was satifsfied but essentially it was broken).

I updated conda to 4.3.24 and checked that our "ensure_conda_channels" setting matched the one in 'galaxy.ini.sample'. Now when I try to reinstall the seq2hla tool, the dependency cannot be installed at all - there seems to be an issue with the R 3.1.2-2 conda package which this needs to pull in:

ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'defaults::r-3.1.2-2'.
PaddingError: Placeholder of length '80' too short in package /XXXXXXXXX/galaxy/production/tool_dependencies/_conda/envs/__seq2HLA@2.2/bin/Rscript.
The package must be rebuilt with conda-build > 2.0.

XXXX... above is the path to the Galaxy installation directory, and the full path does exceed 80 characters. Presumably this worked okay on the local Galaxy install because there the path is shorter than the 80 character limit.

Is there any workaround or fix that I can use to get this working on our production instance?

Also, is it generally safe to update the Galaxy conda installation as I have done? Is there a recommended conda version for Galaxy?

Thanks for your help, best wishes

Peter

--
Peter Briggs [hidden email] Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other 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/


------------------------------

Message: 4
Date: Thu, 11 Jan 2018 08:40:25 -0800
From: Jennifer Hillman-Jackson <[hidden email]>
To: Matthias Enders <[hidden email]>
Cc: Fabian Kaiser <[hidden email]>,
        "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes
Message-ID:
        <CAJ_ABepjC4w7ayYu2Hhj3SnoZ+NkAMiE4EH3=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hello,

Did the suggested help from Biostars help?
https://biostar.usegalaxy.org/p/26197/

Thanks!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Jan 3, 2018 at 6:01 AM, Matthias Enders < [hidden email]> wrote:

> 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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> Von: galaxy-dev [mailto:[hidden email]] Im
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> Betreff: galaxy-dev Digest, Vol 138, Issue 9
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> Today's Topics:
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>    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 <[hidden email]>
> To: Hans-Rudolf Hotz <[hidden email]>
> Cc: galaxy-dev <[hidden email]>
> 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 <[hidden email]> 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 <[hidden email]
> >> <mailto:[hidden email]>> 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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