date:20160223

Re: [galaxy-dev] cleanup

2016-02-23 Thread Rathert , Philipp , Dr .

Dear Nicola,



thanks it worked. 





cheers,



Philipp

-Original message-
From: Nicola Soranzo 
Sent: Tuesday 23rd February 2016 20:35
To: Rathert, Philipp, Dr. ; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] cleanup

 
 Hi Philipp,
 please alway reply to the mailing list.
 
 I'm not using Docker, but if Galaxy is in the /galaxy-central/ directory and 
its version is 16.01, then:
 
 $ cd /galaxy-central/
 $ . .venv/bin/activate
 
$ python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -30 
-1
 $ deactivate
 
 The command ". .venv/bin/activate" will activate the virtualenv installed in 
/galaxy-central/.venv/ , "deactivate" will deactivate it.
 
 Cheers,
 Nicola
 
 On 23/02/16 19:14, Rathert, Philipp, Dr. wrote:
 
 
Hi Nicola,
 
Could you be a bit more specific?
 
I guess i activate this in the specific container but how exactly?
 

 
 
Thanks a lot for your help.
 

 
 

 
 
Cheers,
 

 
 
Philipp
 ---Philipp on the road---
 

 Am 23.02.2016 um 16:20 schrieb Nicola Soranzo :
 
 
 
 

 Hi Philipp,
 if you are using Galaxy release 16.01, you should load the virtualenv
 before running the cleanup script, e.g.:
 
 $ cd GALAXY_HOME
 $ . .venv/bin/activate
 $ python scripts/cleanup_datasets/cleanup_datasets.py ...
 
 Cheers,
 Nicola
 
 On 23/02/16 15:07, Hans-Rudolf Hotz wrote:
 > Hi Philipp
 >
 >
 > point 1 : that's as expected - good.
 >
 > point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?
 >
 >
 > Hans-Rudolf
 >
 >
 >
 >
 > On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:
 >> Dear Hans-Rudolf,
 >>
 >> thanks a lot for your help.
 >>
 >> I did as you suggested:
 >>
 >> 1. when I go into the scripts folder I get the error message you
 >> guessed:
 >> root@galaxy:/galaxy-central/scripts# python
 >> cleanup_datasets/cleanup_datasets.py
 >> /export/galaxy-central/config/galaxy.ini -d -30 -1
 >> Traceback (most recent call last):
 >> File "cleanup_datasets/cleanup_datasets.py", line 21, in 
 >>   import galaxy.config
 >> ImportError: No module named galaxy.config
 >>
 >>
 >> 2. from the root directory I recieve the following error message:
 >> root@galaxy:/galaxy-central# python
 >> scripts/cleanup_datasets/cleanup_datasets.py
 >> /export/galaxy-central/config/galaxy.ini -d -60 -1
 >> Traceback (most recent call last):
 >> File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in
 >> 
 >>   import galaxy.config
 >> File "/galaxy-central/lib/galaxy/config.py", line 21, in 
 >>   from galaxy.util.dbkeys import GenomeBuilds
 >> File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in
 >> 
 >>   from galaxy.util.object_wrapper import sanitize_lists_to_string
 >> File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line
 >> 45, in
 >> 
 >>   from six.moves import UserDict
 >> ImportError: cannot import name UserDict
 >>
 >> Any idea what this means? I thought this should be automatically
 >> installed with python...
 >>
 >> Cheers,
 >>
 >> Philipp
 >>
 >>  -Original message-
 >>  *From:* Hans-Rudolf Hotz 
 >>  *Sent:* Monday 22nd February 2016 17:09
 >>  *To:* Rathert, Philipp, Dr. ;
 >>  galaxy-dev@lists.galaxyproject.org
 >>  *Subject:* Re: [galaxy-dev] cleanup
 >>
 >>  Hi Philipp
 >>
 >>  > Since the new galaxy version, I am unable to perform a cleanup
 >> anymore.
 >>  >
 >>  >  From the galaxy root directory I want to start the script
 >>  > cleanup_datasets.py with the following line:
 >>  >
 >>  > $ python cleanup_datasets.py
 >> /export/galaxy-central/config/galaxy.ini -d
 >>  > -60 -1
 >>  >
 >>  > I get the error message:
 >>  >
 >>  > Can’t open file ‘cleanup_datasets.py’: no such file or directory.
 >>
 >>  Have you tried:
 >>
 >>  $ python scripts/cleanup_datasets/cleanup_datasets.py
 >>  /export/galaxy-central/config/galaxy.ini -d -60 -1
 >>
 >>  > But when I go into the folder in which the script is located
 >> it doesn’t
 >>  > work as well.
 >>
 >>  what is the error this time? Is it "ImportError: No module named
 >> galaxy"?
 >>
 >>
 >>  Regards, Hans-Rudolf
 >>
 >>
 >>  > For your information: we are running the latest
 >> docker-galaxy-stable
 >>  > version.
 >>  >
 >>  > I hope somebody has an idea.
 >>  >
 >>  > Cheers,
 >>  >
 >>  > Philipp
 >>  >
 >>  > --
 >>  >
 >>  > Philipp Rathert, PhD
 >>  >
 >>  > Institute of Biochemistry
 >>  >
 >>  > University Stuttgart
 >>  >
 >>  > Pfaffenwaldring 55
 >>  >
 >>  > D-70569 Stuttgart
 >>  >
 >>  > Germany
 >>  >
 >>  > Tel: +49 711 685 64388
 >>  >
 >>  > Fax: +49 711 685 64392
 >>  >
 >>  > philipp.rath...@ibc.uni-stuttgart.de
 >>  > 
 >>  >
 >>  > http://www.ibc.uni-stuttgart.de/
 >>  >
 >>  > http

Re: [galaxy-dev] cleanup

2016-02-23 Thread Nicola Soranzo


Hi Philipp,
please alway reply to the mailing list.

I'm not using Docker, but if Galaxy is in the /galaxy-central/ directory 
and its version is 16.01, then:


$ cd /galaxy-central/
$ . .venv/bin/activate
$ python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -30 -1

$ deactivate

The command ". .venv/bin/activate" will activate the virtualenv 
installed in /galaxy-central/.venv/ , "deactivate" will deactivate it.


Cheers,
Nicola

On 23/02/16 19:14, Rathert, Philipp, Dr. wrote:

Hi Nicola,
Could you be a bit more specific?
I guess i activate this in the specific container but how exactly?

Thanks a lot for your help.


Cheers,

Philipp
---Philipp on the road---

Am 23.02.2016 um 16:20 schrieb Nicola Soranzo >:



Hi Philipp,
if you are using Galaxy release 16.01, you should load the virtualenv
before running the cleanup script, e.g.:

$ cd GALAXY_HOME
$ . .venv/bin/activate
$ python scripts/cleanup_datasets/cleanup_datasets.py ...

Cheers,
Nicola

On 23/02/16 15:07, Hans-Rudolf Hotz wrote:
> Hi Philipp
>
>
> point 1 : that's as expected - good.
>
> point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?
>
>
> Hans-Rudolf
>
>
>
>
> On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:
>> Dear Hans-Rudolf,
>>
>> thanks a lot for your help.
>>
>> I did as you suggested:
>>
>> 1. when I go into the scripts folder I get the error message you
>> guessed:
>> root@galaxy:/galaxy-central/scripts# python
>> cleanup_datasets/cleanup_datasets.py
>> /export/galaxy-central/config/galaxy.ini -d -30 -1
>> Traceback (most recent call last):
>> File "cleanup_datasets/cleanup_datasets.py", line 21, in 
>>   import galaxy.config
>> ImportError: No module named galaxy.config
>>
>>
>> 2. from the root directory I recieve the following error message:
>> root@galaxy:/galaxy-central# python
>> scripts/cleanup_datasets/cleanup_datasets.py
>> /export/galaxy-central/config/galaxy.ini -d -60 -1
>> Traceback (most recent call last):
>> File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in
>> 
>>   import galaxy.config
>> File "/galaxy-central/lib/galaxy/config.py", line 21, in 
>>   from galaxy.util.dbkeys import GenomeBuilds
>> File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in
>> 
>>   from galaxy.util.object_wrapper import sanitize_lists_to_string
>> File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line
>> 45, in
>> 
>>   from six.moves import UserDict
>> ImportError: cannot import name UserDict
>>
>> Any idea what this means? I thought this should be automatically
>> installed with python...
>>
>> Cheers,
>>
>> Philipp
>>
>>  -Original message-
>>  *From:* Hans-Rudolf Hotz mailto:h...@fmi.ch>>
>>  *Sent:* Monday 22nd February 2016 17:09
>>  *To:* Rathert, Philipp, Dr. 
>;
>> galaxy-dev@lists.galaxyproject.org 


>>  *Subject:* Re: [galaxy-dev] cleanup
>>
>>  Hi Philipp
>>
>>  > Since the new galaxy version, I am unable to perform a cleanup
>> anymore.
>>  >
>>  >  From the galaxy root directory I want to start the script
>>  > cleanup_datasets.py with the following line:
>>  >
>>  > $ python cleanup_datasets.py
>> /export/galaxy-central/config/galaxy.ini -d
>>  > -60 -1
>>  >
>>  > I get the error message:
>>  >
>>  > Can’t open file ‘cleanup_datasets.py’: no such file or 
directory.

>>
>>  Have you tried:
>>
>>  $ python scripts/cleanup_datasets/cleanup_datasets.py
>>  /export/galaxy-central/config/galaxy.ini -d -60 -1
>>
>>  > But when I go into the folder in which the script is located
>> it doesn’t
>>  > work as well.
>>
>>  what is the error this time? Is it "ImportError: No module named
>> galaxy"?
>>
>>
>>  Regards, Hans-Rudolf
>>
>>
>>  > For your information: we are running the latest
>> docker-galaxy-stable
>>  > version.
>>  >
>>  > I hope somebody has an idea.
>>  >
>>  > Cheers,
>>  >
>>  > Philipp
>>  >
>>  > --
>>  >
>>  > Philipp Rathert, PhD
>>  >
>>  > Institute of Biochemistry
>>  >
>>  > University Stuttgart
>>  >
>>  > Pfaffenwaldring 55
>>  >
>>  > D-70569 Stuttgart
>>  >
>>  > Germany
>>  >
>>  > Tel: +49 711 685 64388
>>  >
>>  > Fax: +49 711 685 64392
>>  >
>>  > philipp.rath...@ibc.uni-stuttgart.de 


>>  > 
>>  >
>>  > http://www.ibc.uni-stuttgart.de/
>>  >
>>  > 
http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en

>>  >
>>  >
>>  >
>>  > ___
>>  > Please keep all replies on the list by using "reply all"
>>  > in your mail clie

Re: [galaxy-dev] correctly installing to toolshed

2016-02-23 Thread Xianrong Wong

Hi Bjoern, it's stored in the same folder as the .xml

Hi Gildas, that is the tool.

Thanks!

On Tue, Feb 23, 2016 at 12:43 PM, Gildas Le Corguillé <
lecorgui...@sb-roscoff.fr> wrote:

> Is it this tool :
> https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_with_same_score/c19a0a942e1b
>
> Gildas
>
> -
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)
>
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81
> http://abims.sb-roscoff.fr
> --
>
>
>
> Le 23 févr. 2016 à 18:35, Björn Grüning  a
> écrit :
>
> Hi,
>
> is the script rm_consecutive_sameScore.pl part of your TS repo and next
> to your tool XML file or where is it stored?
>
> Thanks,
> Bjoern
>
> Am 23.02.2016 um 17:46 schrieb Xianrong Wong:
>
> Hi, I'm new to publishing tools/repository on the toolshed.  I have used
> planemo and lint and tests as well as serve all worked.  I was able to
> use the tool.  However, when I uploaded it onto the test tool shed and
> imported the tool on a cloud instance, I keep getting this error when
> running job:
>
> Fatal error: Exit code 2 () Can't open perl script
> "rm_consecutive_sameScore.pl": No such file or directory
>
>
>
> Please advise! I've been downloading and looking at what others did but
> I still can't figure this out.
>
>
>
> I've attached my .xml file and here are some of the commands I used to
> upload the tool.
>
> planemo shed_create --shed_target testtoolshed
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
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>
>
>
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Re: [galaxy-dev] correctly installing to toolshed

2016-02-23 Thread Gildas Le Corguillé

Is it this tool : 
https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_with_same_score/c19a0a942e1b

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 23 févr. 2016 à 18:35, Björn Grüning  a écrit :
> 
> Hi,
> 
> is the script rm_consecutive_sameScore.pl part of your TS repo and next
> to your tool XML file or where is it stored?
> 
> Thanks,
> Bjoern
> 
> Am 23.02.2016 um 17:46 schrieb Xianrong Wong:
>> Hi, I'm new to publishing tools/repository on the toolshed.  I have used
>> planemo and lint and tests as well as serve all worked.  I was able to
>> use the tool.  However, when I uploaded it onto the test tool shed and
>> imported the tool on a cloud instance, I keep getting this error when
>> running job:
>> 
>> Fatal error: Exit code 2 () Can't open perl script
>> "rm_consecutive_sameScore.pl": No such file or directory
>> 
>> 
>> 
>> Please advise! I've been downloading and looking at what others did but
>> I still can't figure this out.
>> 
>> 
>> 
>> I've attached my .xml file and here are some of the commands I used to
>> upload the tool.
>> 
>> planemo shed_create --shed_target testtoolshed
>> 
>> 
>> 
>> ___
>> 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/

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Re: [galaxy-dev] correctly installing to toolshed

2016-02-23 Thread Björn Grüning

Hi,

is the script rm_consecutive_sameScore.pl part of your TS repo and next
to your tool XML file or where is it stored?

Thanks,
Bjoern

Am 23.02.2016 um 17:46 schrieb Xianrong Wong:
> Hi, I'm new to publishing tools/repository on the toolshed.  I have used
> planemo and lint and tests as well as serve all worked.  I was able to
> use the tool.  However, when I uploaded it onto the test tool shed and
> imported the tool on a cloud instance, I keep getting this error when
> running job:
> 
> Fatal error: Exit code 2 () Can't open perl script
> "rm_consecutive_sameScore.pl": No such file or directory
> 
>  
> 
> Please advise! I've been downloading and looking at what others did but
> I still can't figure this out.
> 
> 
> 
> I've attached my .xml file and here are some of the commands I used to
> upload the tool.
> 
> planemo shed_create --shed_target testtoolshed
> 
> 
> 
> ___
> 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] correctly installing to toolshed

2016-02-23 Thread Xianrong Wong

Hi Gildas,
   thank you for the prompt reply!  I actually have tried
multiple paths to the script, even just the script name as you suggested
but it's always giving the same error of "no such file or directory".



On Tue, Feb 23, 2016 at 11:51 AM, Gildas Le Corguillé <
lecorgui...@sb-roscoff.fr> wrote:

> Hi,
>
> I think that you don’t need :
>
> .$__tool_directory__/
>
> rm_consecutive_sameScore.pl "$input1"
> "$output1"
> seems enough if you join the script .pl with your wrapper .xml
>
> Gildas
>
> -
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)
>
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81
> http://abims.sb-roscoff.fr
> --
>
>
>
> Le 23 févr. 2016 à 17:46, Xianrong Wong  a écrit :
>
> 
>
>
>
___
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in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] correctly installing to toolshed

2016-02-23 Thread Gildas Le Corguillé

Hi,

I think that you don’t need :

.$__tool_directory__/

rm_consecutive_sameScore.pl "$input1" 
"$output1"
seems enough if you join the script .pl with your wrapper .xml

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 23 févr. 2016 à 17:46, Xianrong Wong  a écrit :
> 
> 

___
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[galaxy-dev] correctly installing to toolshed

2016-02-23 Thread Xianrong Wong

Hi, I'm new to publishing tools/repository on the toolshed.  I have used
planemo and lint and tests as well as serve all worked.  I was able to use
the tool.  However, when I uploaded it onto the test tool shed and imported
the tool on a cloud instance, I keep getting this error when running job:

Fatal error: Exit code 2 () Can't open perl script
"rm_consecutive_sameScore.pl": No such file or directory



Please advise! I've been downloading and looking at what others did but I
still can't figure this out.



I've attached my .xml file and here are some of the commands I used to
upload the tool.

planemo shed_create --shed_target testtoolshed






   .$__tool_directory__/rm_consecutive_sameScore.pl "$input1" "$output1"
   















@misc{renameTODO,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {TODO},
  url = {manuscript in preparation},
}


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Re: [galaxy-dev] cleanup

2016-02-23 Thread Nicola Soranzo


Hi Philipp,
if you are using Galaxy release 16.01, you should load the virtualenv 
before running the cleanup script, e.g.:


$ cd GALAXY_HOME
$ . .venv/bin/activate
$ python scripts/cleanup_datasets/cleanup_datasets.py ...

Cheers,
Nicola

On 23/02/16 15:07, Hans-Rudolf Hotz wrote:

Hi Philipp


point 1 : that's as expected - good.

point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?


Hans-Rudolf




On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:

Dear Hans-Rudolf,

thanks a lot for your help.

I did as you suggested:

1. when I go into the scripts folder I get the error message you 
guessed:

root@galaxy:/galaxy-central/scripts# python
cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -30 -1
Traceback (most recent call last):
File "cleanup_datasets/cleanup_datasets.py", line 21, in 
  import galaxy.config
ImportError: No module named galaxy.config


2. from the root directory I recieve the following error message:
root@galaxy:/galaxy-central# python
scripts/cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -60 -1
Traceback (most recent call last):
File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in 


  import galaxy.config
File "/galaxy-central/lib/galaxy/config.py", line 21, in 
  from galaxy.util.dbkeys import GenomeBuilds
File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in 


  from galaxy.util.object_wrapper import sanitize_lists_to_string
File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line 
45, in


  from six.moves import UserDict
ImportError: cannot import name UserDict

Any idea what this means? I thought this should be automatically
installed with python...

Cheers,

Philipp

 -Original message-
 *From:* Hans-Rudolf Hotz 
 *Sent:* Monday 22nd February 2016 17:09
 *To:* Rathert, Philipp, Dr. ;
 galaxy-dev@lists.galaxyproject.org
 *Subject:* Re: [galaxy-dev] cleanup

 Hi Philipp

 > Since the new galaxy version, I am unable to perform a cleanup 
anymore.

 >
 >  From the galaxy root directory I want to start the script
 > cleanup_datasets.py with the following line:
 >
 > $ python cleanup_datasets.py 
/export/galaxy-central/config/galaxy.ini -d

 > -60 -1
 >
 > I get the error message:
 >
 > Can’t open file ‘cleanup_datasets.py’: no such file or directory.

 Have you tried:

 $ python scripts/cleanup_datasets/cleanup_datasets.py
 /export/galaxy-central/config/galaxy.ini -d -60 -1

 > But when I go into the folder in which the script is located 
it doesn’t

 > work as well.

 what is the error this time? Is it "ImportError: No module named 
galaxy"?



 Regards, Hans-Rudolf


 > For your information: we are running the latest 
docker-galaxy-stable

 > version.
 >
 > I hope somebody has an idea.
 >
 > Cheers,
 >
 > Philipp
 >
 > --
 >
 > Philipp Rathert, PhD
 >
 > Institute of Biochemistry
 >
 > University Stuttgart
 >
 > Pfaffenwaldring 55
 >
 > D-70569 Stuttgart
 >
 > Germany
 >
 > Tel: +49 711 685 64388
 >
 > Fax: +49 711 685 64392
 >
 > philipp.rath...@ibc.uni-stuttgart.de
 > 
 >
 > http://www.ibc.uni-stuttgart.de/
 >
 > http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en
 >
 >
 >
 > ___
 > 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] cleanup

2016-02-23 Thread Hans-Rudolf Hotz

Hi Philipp

point 1 : that's as expected - good.

point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?

Hans-Rudolf

On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:

Dear Hans-Rudolf,

thanks a lot for your help.

I did as you suggested:

1. when I go into the scripts folder I get the error message you guessed:
root@galaxy:/galaxy-central/scripts# python
cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -30 -1
Traceback (most recent call last):
File "cleanup_datasets/cleanup_datasets.py", line 21, in 
  import galaxy.config
ImportError: No module named galaxy.config

2. from the root directory I recieve the following error message:
root@galaxy:/galaxy-central# python
scripts/cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -60 -1
Traceback (most recent call last):
File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in 
  import galaxy.config
File "/galaxy-central/lib/galaxy/config.py", line 21, in 
  from galaxy.util.dbkeys import GenomeBuilds
File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in 
  from galaxy.util.object_wrapper import sanitize_lists_to_string
File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line 45, in

  from six.moves import UserDict
ImportError: cannot import name UserDict

Any idea what this means? I thought this should be automatically
installed with python...

Cheers,

Philipp

 -Original message-
 *From:* Hans-Rudolf Hotz 
 *Sent:* Monday 22nd February 2016 17:09
 *To:* Rathert, Philipp, Dr. ;
 galaxy-dev@lists.galaxyproject.org
 *Subject:* Re: [galaxy-dev] cleanup

 Hi Philipp

 > Since the new galaxy version, I am unable to perform a cleanup anymore.
 >
 >  From the galaxy root directory I want to start the script
 > cleanup_datasets.py with the following line:
 >
 > $ python cleanup_datasets.py /export/galaxy-central/config/galaxy.ini -d
 > -60 -1
 >
 > I get the error message:
 >
 > Can’t open file ‘cleanup_datasets.py’: no such file or directory.

 Have you tried:

 $ python scripts/cleanup_datasets/cleanup_datasets.py
 /export/galaxy-central/config/galaxy.ini -d -60 -1

 > But when I go into the folder in which the script is located it doesn’t
 > work as well.

 what is the error this time? Is it "ImportError: No module named galaxy"?

 Regards, Hans-Rudolf

 > For your information: we are running the latest docker-galaxy-stable
 > version.
 >
 > I hope somebody has an idea.
 >
 > Cheers,
 >
 > Philipp
 >
 > --
 >
 > Philipp Rathert, PhD
 >
 > Institute of Biochemistry
 >
 > University Stuttgart
 >
 > Pfaffenwaldring 55
 >
 > D-70569 Stuttgart
 >
 > Germany
 >
 > Tel: +49 711 685 64388
 >
 > Fax: +49 711 685 64392
 >
 > philipp.rath...@ibc.uni-stuttgart.de
 > 
 >
 > http://www.ibc.uni-stuttgart.de/
 >
 > http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en
 >
 >
 >
 > ___
 > 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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 >http://galaxyproject.org/search/mailinglists/
 >

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Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

2016-02-23 Thread Nate Coraor

On Tue, Feb 23, 2016 at 4:04 AM, Peter Cock 
wrote:

> On Mon, Feb 22, 2016 at 9:02 PM, Nate Coraor  wrote:
> > On Mon, Feb 22, 2016 at 5:54 AM, Peter Cock 
> > wrote:
> >>
> >> Hi all,
> >>
> >> Last week at the Galaxy Admins video hangout Nate gave an
> >> overview of the way Python dependency handling is changing
> >> from using egg files to using wheel files instead - slide links at:
> >>
> >> ...
> >>
> >> Recently we've been trying to setup a replacement Galaxy instance
> >> where jobs are submitted to our SGE cluster as the linux user
> >> requesting the job. This has been a bumpy road, ...
> >>
> >> ...
> >>
> >> Clearly with Galaxy v16.01 the eggs and $PYTHON_EGG_CACHE
> >> will go away. What happens with wheels, Python virtual environments,
> >> and running jobs as the real user?
> >
> >
> > Hi Peter,
> >
> > Unlike eggs, which can be installed in their package format (as a single
> > .egg file) and used in place, wheels are unpacked and their contents
> reside
> > in the virtualenv's site-packages just as if you had `python setup.py
> > install`ed them, there's no cache directory. The "real user" should be
> able
> > to use Galaxy's virtualenv as long as the appropriate read/execute
> > permissions are set on a common group or other.
> >
> > Galaxy's virtualenv is passed down to the jobs when possible:
> >
> >
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh#L17
> >
> > If you need to create a separate virtualenv for jobs to use, you can do
> this
> > with an  tag on the destination:
> >
> >
> >
> https://docs.galaxyproject.org/en/release_16.01/admin/framework_dependencies.html#galaxy-job-handlers
> >
> > There are instructions in that document on how to create your own Galaxy
> > virtualenv:
> >
> >
> >
> https://docs.galaxyproject.org/en/release_16.01/admin/framework_dependencies.html#managing-dependencies-manually
> >
> > I have not used the "real user" stuff in a very long time so I haven't
> > tested this, but I can't think of any major roadblocks that should
> prevent
> > it from working.
> >
> > --nate
>
> Thanks Nate, this sounds promising - fingers crossed :)
>
> Maybe we should test the pre-release branch for v16.10 out?
>

Yes, I don't expect much to change before the release, which, fingers
crossed, will be tomorrow or Wednesday.


>
> Peter
>
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[galaxy-dev] Docker and issue with shed_tool_conf.xml

2016-02-23 Thread Rathert , Philipp , Dr .

Dear All,



I have a serious problem with installing new tools to our local 
Docker-galaxy-stable instance (latest version).



All tools seem to install without any issue from the tool shed. When I check 
under Manage installed tools they all show a green "installed" button.

However, the local tool shed is not updated anymore. none of the newly 
installed tools show up. It seems the shed_tool_conf.xml file is not updated.

the tools are all found in the folder shed_tools but not under tool-data, not 
sure if this means anything.




A work-around could be to manually enter these tools to the shed_tool_conf.xml 
file but to do this I wasn't able to find the guid for each tool. All other 
parameters are easy.

But this would be quite some effort and I am afraid that something is 
seriously wrong. 



It would be great to get your thoughts on this issue before I kill everything 
and start from scratch.



Thanks a lot.



Cheers,



Philipp 



PS: I am a wet lab scientist please be patient if I don't get everything 
immediately.


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Re: [galaxy-dev] Docker and alpine linux

2016-02-23 Thread Marius van den Beek

Just my 2 cents about this:
I feel your pain, our connection to the docker hub is horrible, it takes an
hour to pull the GIE images ... .
(While it only takes seconds from the cloud ...).
The galaxy docker images are pretty fat, because we use them VM-style, in
principle nothing wrong about that.
So the base-image is about 1.2GB  add a few tools and you're quickly
reaching 5GB.
If in addition you use interactive environments ... add a few GB more.

I think that instead of trying to reduce the size of the base-image, it
might be a better effort to separate the components
into a proxy-image, database image (perhaps 2, one for tools / one for
user-data), galaxy-image,
cluster-image ... and so on. This would allow you to just update the tools
and galaxy image regularly,
plus you could do all the neat docker stuff, like versioning, committing,
rolling updates, streaming database replication, worker scaling ...
It's certainly something I would be interested in.
The other thing is to make sure that the tool dependencies are as slim as
possible. Having many different R packages
and their source lying around makes for a lot of data. Hopefully conda can
alleviate that situation.

Cheers,
Marius

On 23 February 2016 at 09:36, Björn Grüning 
wrote:

> Hi Tiago,
>
> thanks for the heads-up. I also tried alpine some time ago but Galaxy
> needs some external dependencies which Nate is building also with a ppa
> for Debian based systems. So this is not so easy to migrate.
>
> What we could do is to orchestrate the containers and its deps:
>
> https://github.com/bgruening/docker-galaxy-stable/issues/43
>
> But this has the big disadvantages of not sharing the setup with other
> Galaxy installations, like the VM installation from planemo-machine.
>
> So in the end I stoped to make it more modular and tried to share as
> much as possible with other installations of Galaxy and move more and
> more into the ansible-playbook.
>
> Thanks Tiago for trying this,
> Bjoern
>
> Am 23.02.2016 um 05:15 schrieb Tiago Antao:
> > Dear all,
> >
> > This email is mostly to report a negative result, maybe to help others
> > _not_ trying something.
> >
> > I researched the possibility of replacing ubuntu with alpine on the
> > Docker images (alpine seems to be used more and more on docker images,
> > with plenty of official containers now based on it and not on debian).
> >
> > The reason alpine is used, its because it generates very small
> > containers (a bare bones one is below 10 MB). But, due the the large
> > dependencies of galaxy, the gain is negligible. Maybe 200 MB or so. 20%
> > is something, but not a revolution.
> >
> > This being said, for servers with smaller dependencies (a mail server,
> > web, ldap, dns...) alpine really reduces the footprint of docker
> > containers.
> >
> > Tiago
> >
> ___
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> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

2016-02-23 Thread Peter Cock

On Mon, Feb 22, 2016 at 9:02 PM, Nate Coraor  wrote:
> On Mon, Feb 22, 2016 at 5:54 AM, Peter Cock 
> wrote:
>>
>> Hi all,
>>
>> Last week at the Galaxy Admins video hangout Nate gave an
>> overview of the way Python dependency handling is changing
>> from using egg files to using wheel files instead - slide links at:
>>
>> ...
>>
>> Recently we've been trying to setup a replacement Galaxy instance
>> where jobs are submitted to our SGE cluster as the linux user
>> requesting the job. This has been a bumpy road, ...
>>
>> ...
>>
>> Clearly with Galaxy v16.01 the eggs and $PYTHON_EGG_CACHE
>> will go away. What happens with wheels, Python virtual environments,
>> and running jobs as the real user?
>
>
> Hi Peter,
>
> Unlike eggs, which can be installed in their package format (as a single
> .egg file) and used in place, wheels are unpacked and their contents reside
> in the virtualenv's site-packages just as if you had `python setup.py
> install`ed them, there's no cache directory. The "real user" should be able
> to use Galaxy's virtualenv as long as the appropriate read/execute
> permissions are set on a common group or other.
>
> Galaxy's virtualenv is passed down to the jobs when possible:
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh#L17
>
> If you need to create a separate virtualenv for jobs to use, you can do this
> with an  tag on the destination:
>
>
> https://docs.galaxyproject.org/en/release_16.01/admin/framework_dependencies.html#galaxy-job-handlers
>
> There are instructions in that document on how to create your own Galaxy
> virtualenv:
>
>
> https://docs.galaxyproject.org/en/release_16.01/admin/framework_dependencies.html#managing-dependencies-manually
>
> I have not used the "real user" stuff in a very long time so I haven't
> tested this, but I can't think of any major roadblocks that should prevent
> it from working.
>
> --nate

Thanks Nate, this sounds promising - fingers crossed :)

Maybe we should test the pre-release branch for v16.10 out?

Peter
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Re: [galaxy-dev] Docker and alpine linux

2016-02-23 Thread Björn Grüning

Hi Tiago,

thanks for the heads-up. I also tried alpine some time ago but Galaxy
needs some external dependencies which Nate is building also with a ppa
for Debian based systems. So this is not so easy to migrate.

What we could do is to orchestrate the containers and its deps:

https://github.com/bgruening/docker-galaxy-stable/issues/43

But this has the big disadvantages of not sharing the setup with other
Galaxy installations, like the VM installation from planemo-machine.

So in the end I stoped to make it more modular and tried to share as
much as possible with other installations of Galaxy and move more and
more into the ansible-playbook.

Thanks Tiago for trying this,
Bjoern

Am 23.02.2016 um 05:15 schrieb Tiago Antao:
> Dear all,
> 
> This email is mostly to report a negative result, maybe to help others
> _not_ trying something.
> 
> I researched the possibility of replacing ubuntu with alpine on the
> Docker images (alpine seems to be used more and more on docker images,
> with plenty of official containers now based on it and not on debian).
> 
> The reason alpine is used, its because it generates very small
> containers (a bare bones one is below 10 MB). But, due the the large
> dependencies of galaxy, the gain is negligible. Maybe 200 MB or so. 20%
> is something, but not a revolution.
> 
> This being said, for servers with smaller dependencies (a mail server,
> web, ldap, dns...) alpine really reduces the footprint of docker
> containers.
> 
> Tiago
> 
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Re: [galaxy-dev] cleanup

Re: [galaxy-dev] cleanup

Re: [galaxy-dev] correctly installing to toolshed

Re: [galaxy-dev] correctly installing to toolshed

Re: [galaxy-dev] correctly installing to toolshed

Re: [galaxy-dev] correctly installing to toolshed

Re: [galaxy-dev] correctly installing to toolshed

[galaxy-dev] correctly installing to toolshed

Re: [galaxy-dev] cleanup

Re: [galaxy-dev] cleanup

Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

[galaxy-dev] Docker and issue with shed_tool_conf.xml

Re: [galaxy-dev] Docker and alpine linux

Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

Re: [galaxy-dev] Docker and alpine linux

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