Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

2018-01-11 Thread Jennifer Hillman-Jackson 
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 <
m.end...@german-seed-alliance.de> 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: m.end...@german-seed-alliance.de
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -Ursprüngliche Nachricht-
> Von: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im
> Auftrag von galaxy-dev-requ...@lists.galaxyproject.org
> Gesendet: Donnerstag, 21. Dezember 2017 18:00
> An: galaxy-dev@lists.galaxyproject.org
> Betreff: galaxy-dev Digest, Vol 138, Issue 9
>
> Send galaxy-dev mailing list submissions to
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> 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 
> To: Hans-Rudolf Hotz 
> Cc: galaxy-dev 
> Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work
> Message-ID:
>  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  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  >> > 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

Re: [galaxy-dev] Problems installing conda dependencies for seq2hla tool

2018-01-11 Thread Peter Briggs 
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 peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482



From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Peter Briggs [peter.bri...@manchester.ac.uk]
Sent: Friday, January 05, 2018 12:06 PM
To: galaxy-dev@lists.galaxyproject.org
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 
/X/galaxy/production/tool_dependencies/_conda/envs/__seq2HLA@2.2/bin/Rscript.
The package must be rebuilt with conda-build > 2.0.

... 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 peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

2018-01-11 Thread Devon Ryan 
This is presumably the same question elsewhere:
https://biostar.usegalaxy.org/p/26197/
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
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
 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: m.end...@german-seed-alliance.de
>>
>> Firmensitz Köln Amtsgericht Köln, HRB 73844
>>
>> -Ursprüngliche Nachricht- Von: galaxy-dev
>> [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von
>> galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Donnerstag, 21.
>> Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff:
>> galaxy-dev Digest, Vol 138, Issue 9
>>
>> Send galaxy-dev mailing list submissions to
>> galaxy-dev@lists.galaxyproject.org
>>
>> 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
>> galaxy-dev-requ...@lists.galaxyproject.org
>>
>> You can reach the person managing the list at
>> galaxy-dev-ow...@lists.galaxyproject.org
>>
>> 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
>>  To: Hans-Rudolf Hotz  Cc: galaxy-dev
>>  Subject: Re: [galaxy-dev] Galaxy
>> v17.09 impersonation doesn't work Message-ID:
>> 
>> 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 
>> 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 >>> > 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

Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

2018-01-11 Thread Björn Grüning 

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: m.end...@german-seed-alliance.de

Firmensitz Köln Amtsgericht Köln, HRB 73844

-Ursprüngliche Nachricht- Von: galaxy-dev
[mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von
galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Donnerstag, 21.
Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff:
galaxy-dev Digest, Vol 138, Issue 9

Send galaxy-dev mailing list submissions to 
galaxy-dev@lists.galaxyproject.org


To subscribe or unsubscribe via the World Wide Web, visit 
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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
 To: Hans-Rudolf Hotz  Cc: galaxy-dev
 Subject: Re: [galaxy-dev] Galaxy
v17.09 impersonation doesn't work Message-ID: 
 
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 
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 > 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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