Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

[Katherine Beaulieu]

Ok, so I don't give the user the option to select the correct data type to
reduce the amount of stuff the user has to know when using the tool.

I do leave the format as auto and Galaxy just leaves it as the generic data
type 'data'.

As for how the format is defined in Galaxy, I'm not quite sure what the
answer to this question is because I am just testing the tool with really
simple text files, with extension .txt. and it can't seem to pick it up, it
just leaves it as 'data'. Also not quite sure how to test the Python code
in the sniff function outside of Galaxy... (only starting working with
Galaxy 3 weeks ago).

Let me know if I should provide you with the tool config file if that would
be a little more useful. It's quite straightforward
Thanks for helping with this.

On Wed, Jun 29, 2016 at 11:16 AM, Peter Cock 
wrote:

> OK. What happens?
>
> Can you select the correct datatype in the upload tool?
> If not, check the file format definition as some file formats
> are configured not to appear here.
>
> Are you leaving the datatype as "auto"? If so, does
> Galaxy fail to identify the file, and leave it as the
> default generic "data" type, or does Galaxy mis-identify
> it as another type?
>
> Have you looked at the Galaxy logs while doing the
> upload?
>
> How is this file format defined in Galaxy? Did you add it?
> Can you test the Python code in the sniff function outside
> of Galaxy to confirm that works?
>
> If Galaxy wrongly picks another fileformat, check where
> in the datatypes_conf.xml is your file format listed? The
> order the sniffing functions are run is important.
>
> Peter
>
> On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu
>  wrote:
> > I am trying to import a file into galaxy.
> >
> > On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock 
> > wrote:
> >>
> >> The auto-detection is only used when importing a
> >> file into Galaxy (e.g. by uploading it).
> >>
> >> If you are writing a tool which produces output in your
> >> format, then the tool's XML should specify that output
> >> format.
> >>
> >> Which of these are you trying to do? Or both?
> >>
> >> Peter
> >>
> >> On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu
> >>  wrote:
> >> > Hmm, I must have some sort of other logic error which is preventing
> the
> >> > detection of the format. Thanks for the information!
> >> >
> >> > On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <
> p.j.a.c...@googlemail.com>
> >> > wrote:
> >> >>
> >> >> Have you invented your own file format, or are you using
> >> >> an existing file format defined within Galaxy?
> >> >>
> >> >> The Galaxy file formats with automatic detection are all
> >> >> defined via Python classes which define a sniff method.
> >> >>
> >> >> Peter
> >> >>
> >> >> On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu
> >> >>  wrote:
> >> >> > Hi everyone,
> >> >> > I am looking to auto-detect the file format of a file outputted by
> a
> >> >> > python
> >> >> > tool I have written. Does anyone have any idea how to do this? I
> have
> >> >> > tried
> >> >> > setting the format attribute to "auto" with no luck. Let me know if
> >> >> > you
> >> >> > would like to see my tool config file.
> >> >> > Cheers,
> >> >> > Katherine
> >> >> >
> >> >> > ___
> >> >> > 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/mailinglists/
> >> >
> >> >
> >
> >
>
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Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

[Peter Cock]

OK. What happens?

Can you select the correct datatype in the upload tool?
If not, check the file format definition as some file formats
are configured not to appear here.

Are you leaving the datatype as "auto"? If so, does
Galaxy fail to identify the file, and leave it as the
default generic "data" type, or does Galaxy mis-identify
it as another type?

Have you looked at the Galaxy logs while doing the
upload?

How is this file format defined in Galaxy? Did you add it?
Can you test the Python code in the sniff function outside
of Galaxy to confirm that works?

If Galaxy wrongly picks another fileformat, check where
in the datatypes_conf.xml is your file format listed? The
order the sniffing functions are run is important.

Peter

On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu
 wrote:
> I am trying to import a file into galaxy.
>
> On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock 
> wrote:
>>
>> The auto-detection is only used when importing a
>> file into Galaxy (e.g. by uploading it).
>>
>> If you are writing a tool which produces output in your
>> format, then the tool's XML should specify that output
>> format.
>>
>> Which of these are you trying to do? Or both?
>>
>> Peter
>>
>> On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu
>>  wrote:
>> > Hmm, I must have some sort of other logic error which is preventing the
>> > detection of the format. Thanks for the information!
>> >
>> > On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock 
>> > wrote:
>> >>
>> >> Have you invented your own file format, or are you using
>> >> an existing file format defined within Galaxy?
>> >>
>> >> The Galaxy file formats with automatic detection are all
>> >> defined via Python classes which define a sniff method.
>> >>
>> >> Peter
>> >>
>> >> On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu
>> >>  wrote:
>> >> > Hi everyone,
>> >> > I am looking to auto-detect the file format of a file outputted by a
>> >> > python
>> >> > tool I have written. Does anyone have any idea how to do this? I have
>> >> > tried
>> >> > setting the format attribute to "auto" with no luck. Let me know if
>> >> > you
>> >> > would like to see my tool config file.
>> >> > Cheers,
>> >> > Katherine
>> >> >
>> >> > ___
>> >> > 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/mailinglists/
>> >
>> >
>
>
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Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

[Peter Cock]

The auto-detection is only used when importing a
file into Galaxy (e.g. by uploading it).

If you are writing a tool which produces output in your
format, then the tool's XML should specify that output
format.

Which of these are you trying to do? Or both?

Peter

On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu
 wrote:
> Hmm, I must have some sort of other logic error which is preventing the
> detection of the format. Thanks for the information!
>
> On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock 
> wrote:
>>
>> Have you invented your own file format, or are you using
>> an existing file format defined within Galaxy?
>>
>> The Galaxy file formats with automatic detection are all
>> defined via Python classes which define a sniff method.
>>
>> Peter
>>
>> On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu
>>  wrote:
>> > Hi everyone,
>> > I am looking to auto-detect the file format of a file outputted by a
>> > python
>> > tool I have written. Does anyone have any idea how to do this? I have
>> > tried
>> > setting the format attribute to "auto" with no luck. Let me know if you
>> > would like to see my tool config file.
>> > Cheers,
>> > Katherine
>> >
>> > ___
>> > 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/mailinglists/
>
>
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Re: [galaxy-dev] Docker for Mac

[Suderman Keith]

> On Jun 29, 2016, at 7:02 AM, Philipp Rathert 
>  wrote:
> 
> Hi Ido,
> 
> I get no error message, but the command does not change anything. Rights are 
> still assigned to host user and not to postgresql.
> 
> Could it be that, since galaxy and other program were running in a docker 
> container, none of these users are known in the actual host environment?

That could very well be, and it is something I was hoping would be fixed in 
Docker for Mac.  My work around in classic Docker is to make sure 
Galaxy/Postgres use the same GID/UID inside the container as on my host system. 
 However, this requires (as far as I recall) rebuilding the Docker image as 
this is where UID/GID for Galaxy/Postgres are assigned.

Hope that helps,
Keith

> 
> 
> Cheers,
> 
> Philipp
> 
> -Original Message-
> From: Tamir,Ido [mailto:ido.ta...@vbcf.ac.at]
> Sent: Wednesday, June 29, 2016 12:50 PM
> To: Rathert, Philipp, Dr. 
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Docker for Mac
> 
>> 
>> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr.
>>  wrote:
>> 
>> And I have the additional problem that I have to assign ownership
>> rights to the folders in /export and I get the following error:
>> 
>> 
>> chown -R postgres:postgres /postgresql
>> chown: postgres: illegal group name
>> 
> 
> I think on OSX the user/group is _postgres and it should be
>> chown -R _postgres:_postgres /export
> 
> 
>> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr.
>>  wrote:
>> 
>> Dear all I was wondering if anybody has experience running a galaxy
>> production server using docker for mac. I know it's beta testing at
>> the moment but since the Virtual machine environment gave us such a
>> hard time preserving and managing user data etc. I thought I try it anyway...
>> 
>> However, it seems to be not as easy as expected.
>> 
>> after installation of docker I pull the new docker galaxy image with
>> docker pull quay.io/bgruening/galaxy:16.04  When I start a test
>> container with net=host docker run -it --net=host
>> quay.io/bgruening/galaxy:16.04)  I am not able to connect to the
>> galaxy web app and get this  error:
>> 
>> 
>> Starting ProFTP
>> proftpd: ERROR (abnormal termination)
>> 
>> 
>> and
>> 
>> 
>> 
>> ==> /home/galaxy/logs/slurmd.log <==
>> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown
>> host [2016-06-29T08:13:41.440] error: Unable to establish control
>> machine address
>> 
>> 
>> 
>> I then tried to use Kinematik and at least I get the web app running.
>> However, I didn't find the option to change the network settings to
>> net=host
>> 
>> 
>> 
>> And I have the additional problem that I have to assign ownership
>> rights to the folders in /export and I get the following error:
>> 
>> 
>> chown -R postgres:postgres /postgresql
>> chown: postgres: illegal group name
>> 
>> I know these are many issues, but maybe one of you has experience with
>> this and could provide some help.
>> 
>> Thanks a lot,
>> 
>> Philipp
>> 
>> ___
>> 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/mailinglists/
> 
> 
> ___
> 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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> 
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--
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY



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[galaxy-dev] Auto detection of output format Galaxy custom tool

[Katherine Beaulieu]

Hi everyone,
I am looking to auto-detect the file format of a file outputted by a python
tool I have written. Does anyone have any idea how to do this? I have tried
setting the format attribute to "auto" with no luck. Let me know if you
would like to see my tool config file.
Cheers,
Katherine
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Re: [galaxy-dev] Docker for Mac

[Hans-Rudolf Hotz]

> On 29 Jun 2016, at 15:57, Philipp Rathert 
>  wrote:
> 
> Hi Hans-Rudolph,
> This means you use 
> Docker pull bgruening/galaxy-stable:latest to get the image?
>  

yesy

> I just noticed that the “latest” image is 6 weeks old and the other only 9 
> days…
>  
> Anyway, I will try if the problems occur with the old one as well. 
>  
> Did you ever tried to use Docker for mac in a production mode, if yes any 
> idea how to allow acces from other computers in the network?


only used for training and demonstration purposes so far. 
haven’t tried to access it over our network, but don’t see a reason why it 
should not work.

Hans-Rudolf




> Cheers,
>  
> Philipp
>  
> From: Hans-Rudolf Hotz [mailto:hansrudolf.h...@fmi.ch 
> ] 
> Sent: Wednesday, June 29, 2016 3:50 PM
> To: Rathert, Philipp, Dr.  >
> Cc: galaxy-dev@lists.galaxyproject.org 
> 
> Subject: Re: [galaxy-dev] Docker for Mac
>  
> Hi Philipp
>  
> I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have 
> always used the traditional location for the image to fetch from: 
> https://index.docker.io/u/bgruening/galaxy-stable/ 
>    (i.e just following 
> the excellent recipes on https://github.com/bgruening/docker-galaxy-stable 
>  )
>  
> and just by coincidence:  last night I tried 'quay.io/bgruening/galaxy:16.04' 
>  and it didn’t work, but I haven’t  
> investigated why….
>  
> Hans-Rudolf
>  
>  
>> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>> > > wrote:
>>  
>> Dear all I was wondering if anybody has experience running a galaxy 
>> production server using docker for mac. I know it's beta testing at the 
>> moment but since the Virtual machine environment gave us such a hard time 
>> preserving and managing user data etc. I thought I try it anyway...
>> 
>> 
>> However, it seems to be not as easy as expected.
>>  
>> after installation of docker I pull the new docker galaxy image with
>> docker pull quay.io/bgruening/ galaxy:16.04 
>> 
>> 
>> 
>> When I start a test container with net=host
>> docker run -it --net=host quay.io/bgruening/ 
>> galaxy:16.04 ) 
>> 
>> 
>> I am not able to connect to the galaxy web app and get this  error:
>> 
>> 
>> 
>> Starting ProFTP
>> proftpd: ERROR (abnormal termination)
>> 
>> 
>> 
>> 
>> and 
>> 
>> 
>> 
>> 
>> 
>> 
>> ==> /home/galaxy/logs/slurmd.log <==
>> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host
>> [2016-06-29T08:13:41.440] error: Unable to establish control machine address
>> 
>> 
>> 
>> 
>> 
>> 
>> I then tried to use Kinematik and at least I get the web app running. 
>> However, I didn't find the option to change the network settings to net=host
>> 
>> 
>> 
>> 
>> 
>> 
>> And I have the additional problem that I have to assign ownership rights to 
>> the folders in /export and I get the following error:
>> 
>> 
>> 
>> 
>> chown -R postgres:postgres  /postgresql
>> chown: postgres: illegal group name
>> 
>> 
>> I know these are many issues, but maybe one of you has experience with this 
>> and could provide some help.
>> 
>> 
>> Thanks a lot,
>> 
>> 
>> Philipp
>> 
>> 
>> 
>> ___
>> 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/mailinglists/ 
>> 
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Re: [galaxy-dev] Docker for Mac

[Philipp Rathert]

Hi Hans-Rudolph,

This means you use 

Docker pull bgruening/galaxy-stable:latest to get the image?

 

I just noticed that the “latest” image is 6 weeks old and the other only 9 days…

 

Anyway, I will try if the problems occur with the old one as well. 

 

Did you ever tried to use Docker for mac in a production mode, if yes any idea 
how to allow acces from other computers in the network?

 

Cheers,

 

Philipp

 

From: Hans-Rudolf Hotz [mailto:hansrudolf.h...@fmi.ch] 
Sent: Wednesday, June 29, 2016 3:50 PM
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Docker for Mac

 

Hi Philipp

 

I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always 
used the traditional location for the image to fetch from: 
https://index.docker.io/u/bgruening/galaxy-stable/   (i.e just following the 
excellent recipes on https://github.com/bgruening/docker-galaxy-stable )

 

and just by coincidence:  last night I tried ' 
 quay.io/bgruening/galaxy:16.04' and it 
didn’t work, but I haven’t  investigated why….

 

Hans-Rudolf

 

 

On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
 > wrote:

 

Dear all I was wondering if anybody has experience running a galaxy production 
server using docker for mac. I know it's beta testing at the moment but since 
the Virtual machine environment gave us such a hard time preserving and 
managing user data etc. I thought I try it anyway...





However, it seems to be not as easy as expected.

 

after installation of docker I pull the new docker galaxy image with

docker pull quay.io/bgruening/  galaxy:16.04





When I start a test container with net=host

docker run -it --net=host quay.io/bgruening/  
galaxy:16.04) 





I am not able to connect to the galaxy web app and get this  error:







Starting ProFTP

proftpd: ERROR (abnormal termination)









and 













==> /home/galaxy/logs/slurmd.log <==

[2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host

[2016-06-29T08:13:41.440] error: Unable to establish control machine address













I then tried to use Kinematik and at least I get the web app running. However, 
I didn't find the option to change the network settings to net=host













And I have the additional problem that I have to assign ownership rights to the 
folders in /export and I get the following error:









chown -R   postgres:postgres /postgresql

chown: postgres: illegal group name





I know these are many issues, but maybe one of you has experience with this and 
could provide some help.





Thanks a lot,





Philipp







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Re: [galaxy-dev] Docker for Mac

[Hans-Rudolf Hotz]

Hi Philipp

I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always 
used the traditional location for the image to fetch from: 
https://index.docker.io/u/bgruening/galaxy-stable/ 
   (i.e just following the 
excellent recipes on https://github.com/bgruening/docker-galaxy-stable 
 )

and just by coincidence:  last night I tried 'quay.io/bgruening/galaxy:16.04' 
 and it didn’t work, but I haven’t  
investigated why….

Hans-Rudolf


> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>  wrote:
> 
> Dear all I was wondering if anybody has experience running a galaxy 
> production server using docker for mac. I know it's beta testing at the 
> moment but since the Virtual machine environment gave us such a hard time 
> preserving and managing user data etc. I thought I try it anyway...
> 
> However, it seems to be not as easy as expected.
> 
> after installation of docker I pull the new docker galaxy image with
> docker pull quay.io/bgruening/galaxy:16.04 
> 
> When I start a test container with net=host
> docker run -it --net=host quay.io/bgruening/galaxy:16.04 ) 
> 
> I am not able to connect to the galaxy web app and get this  error:
> 
> 
> Starting ProFTP
> proftpd: ERROR (abnormal termination)
> 
> 
> and 
> 
> 
> 
> ==> /home/galaxy/logs/slurmd.log <==
> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host
> [2016-06-29T08:13:41.440] error: Unable to establish control machine address
> 
> 
> 
> I then tried to use Kinematik and at least I get the web app running. 
> However, I didn't find the option to change the network settings to net=host
> 
> 
> 
> And I have the additional problem that I have to assign ownership rights to 
> the folders in /export and I get the following error:
> 
> 
> chown -R postgres:postgres  /postgresql
> chown: postgres: illegal group name
> 
> I know these are many issues, but maybe one of you has experience with this 
> and could provide some help.
> 
> Thanks a lot,
> 
> Philipp
> 
> ___
> 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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> 
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Re: [galaxy-dev] Docker for Mac

[Tamir,Ido]

I don’t know anything about docker - yet.
best,
ido

> On 29 Jun 2016, at 13:02, Philipp Rathert 
>  wrote:
> 
> Hi Ido,
> 
> I get no error message, but the command does not change anything. Rights are 
> still assigned to host user and not to postgresql.
> 
> Could it be that, since galaxy and other program were running in a docker 
> container, none of these users are known in the actual host environment?
> 
> 
> Cheers,
> 
> Philipp
> 
> -Original Message-
> From: Tamir,Ido [mailto:ido.ta...@vbcf.ac.at] 
> Sent: Wednesday, June 29, 2016 12:50 PM
> To: Rathert, Philipp, Dr. 
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Docker for Mac
> 
>> 
>> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>>  wrote:
>> 
>> And I have the additional problem that I have to assign ownership 
>> rights to the folders in /export and I get the following error:
>> 
>> 
>> chown -R postgres:postgres /postgresql
>> chown: postgres: illegal group name
>> 
> 
> I think on OSX the user/group is _postgres and it should be
>> chown -R _postgres:_postgres /export
> 
> 
>> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>>  wrote:
>> 
>> Dear all I was wondering if anybody has experience running a galaxy 
>> production server using docker for mac. I know it's beta testing at 
>> the moment but since the Virtual machine environment gave us such a 
>> hard time preserving and managing user data etc. I thought I try it anyway...
>> 
>> However, it seems to be not as easy as expected.
>> 
>> after installation of docker I pull the new docker galaxy image with 
>> docker pull quay.io/bgruening/galaxy:16.04  When I start a test 
>> container with net=host docker run -it --net=host 
>> quay.io/bgruening/galaxy:16.04)  I am not able to connect to the 
>> galaxy web app and get this  error:
>> 
>> 
>> Starting ProFTP
>> proftpd: ERROR (abnormal termination)
>> 
>> 
>> and
>> 
>> 
>> 
>> ==> /home/galaxy/logs/slurmd.log <==
>> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown 
>> host [2016-06-29T08:13:41.440] error: Unable to establish control 
>> machine address
>> 
>> 
>> 
>> I then tried to use Kinematik and at least I get the web app running. 
>> However, I didn't find the option to change the network settings to 
>> net=host
>> 
>> 
>> 
>> And I have the additional problem that I have to assign ownership 
>> rights to the folders in /export and I get the following error:
>> 
>> 
>> chown -R postgres:postgres /postgresql
>> chown: postgres: illegal group name
>> 
>> I know these are many issues, but maybe one of you has experience with 
>> this and could provide some help.
>> 
>> Thanks a lot,
>> 
>> Philipp
>> 
>> ___
>> 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/
>> 
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>> http://galaxyproject.org/search/mailinglists/
> 
> 

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Re: [galaxy-dev] Docker for Mac

[Philipp Rathert]

Hi Ido,

I get no error message, but the command does not change anything. Rights are 
still assigned to host user and not to postgresql.

Could it be that, since galaxy and other program were running in a docker 
container, none of these users are known in the actual host environment?


Cheers,

Philipp

-Original Message-
From: Tamir,Ido [mailto:ido.ta...@vbcf.ac.at] 
Sent: Wednesday, June 29, 2016 12:50 PM
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Docker for Mac

>
> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>  wrote:
>
> And I have the additional problem that I have to assign ownership 
> rights to the folders in /export and I get the following error:
> 
>
> chown -R postgres:postgres /postgresql
> chown: postgres: illegal group name
>

I think on OSX the user/group is _postgres and it should be
> chown -R _postgres:_postgres /export


> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>  wrote:
>
> Dear all I was wondering if anybody has experience running a galaxy 
> production server using docker for mac. I know it's beta testing at 
> the moment but since the Virtual machine environment gave us such a 
> hard time preserving and managing user data etc. I thought I try it anyway...
>
> However, it seems to be not as easy as expected.
>
> after installation of docker I pull the new docker galaxy image with 
> docker pull quay.io/bgruening/galaxy:16.04  When I start a test 
> container with net=host docker run -it --net=host 
> quay.io/bgruening/galaxy:16.04)  I am not able to connect to the 
> galaxy web app and get this  error:
>
> 
> Starting ProFTP
> proftpd: ERROR (abnormal termination)
>
> 
> and
>
>
>
> ==> /home/galaxy/logs/slurmd.log <==
> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown 
> host [2016-06-29T08:13:41.440] error: Unable to establish control 
> machine address
>
>
>
> I then tried to use Kinematik and at least I get the web app running. 
> However, I didn't find the option to change the network settings to 
> net=host
>
>
>
> And I have the additional problem that I have to assign ownership 
> rights to the folders in /export and I get the following error:
> 
>
> chown -R postgres:postgres /postgresql
> chown: postgres: illegal group name
>
> I know these are many issues, but maybe one of you has experience with 
> this and could provide some help.
>
> Thanks a lot,
>
> Philipp
>
> ___
> 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/mailinglists/


___
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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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Docker for Mac

[Tamir,Ido]

> 
> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>  wrote:
> 
> And I have the additional problem that I have to assign ownership rights to 
> the folders in /export and I get the following error:
> 
> 
> chown -R postgres:postgres /postgresql
> chown: postgres: illegal group name
> 

I think on OSX the user/group is _postgres and it should be
> chown -R _postgres:_postgres /export


> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>  wrote:
> 
> Dear all I was wondering if anybody has experience running a galaxy 
> production server using docker for mac. I know it's beta testing at the 
> moment but since the Virtual machine environment gave us such a hard time 
> preserving and managing user data etc. I thought I try it anyway...
> 
> However, it seems to be not as easy as expected.
> 
> after installation of docker I pull the new docker galaxy image with
> docker pull quay.io/bgruening/galaxy:16.04
> 
> When I start a test container with net=host
> docker run -it --net=host quay.io/bgruening/galaxy:16.04) 
> 
> I am not able to connect to the galaxy web app and get this  error:
> 
> 
> Starting ProFTP
> proftpd: ERROR (abnormal termination)
> 
> 
> and 
> 
> 
> 
> ==> /home/galaxy/logs/slurmd.log <==
> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host
> [2016-06-29T08:13:41.440] error: Unable to establish control machine address
> 
> 
> 
> I then tried to use Kinematik and at least I get the web app running. 
> However, I didn't find the option to change the network settings to net=host
> 
> 
> 
> And I have the additional problem that I have to assign ownership rights to 
> the folders in /export and I get the following error:
> 
> 
> chown -R postgres:postgres /postgresql
> chown: postgres: illegal group name
> 
> I know these are many issues, but maybe one of you has experience with this 
> and could provide some help.
> 
> Thanks a lot,
> 
> Philipp
> 
> ___
> 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/mailinglists/

___
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/mailinglists/