[galaxy-dev] CleanUp Datastets ERROR since update from bitbucket to git

[julie dubois]

Hi all,

I've recently updated my local instance of Galaxy from bitbucket to
git. It seems to work fine. No error when we run galaxy.
But I've been tried to cleanup datasets and when I ran this command :

python scripts/cleanup_datasets/cleanup_datasets_Redirection.py
universe_wsgi.ini -d 0 -1 -r $@

I have error in python module like this :
Traceback (most recent call last):
  File "scripts/cleanup_datasets/cleanup_datasets_Redirection.py",
line 23, in 
import galaxy.model.mapping
  File "/data/galaxy-dist/lib/galaxy/model/mapping.py", line 19, in 
from galaxy.model.custom_types import JSONType, MetadataType,
TrimmedString, UUIDType
  File "/data/galaxy-dist/lib/galaxy/model/custom_types.py", line 13,
in 
from galaxy import app
  File "/data/galaxy-dist/lib/galaxy/app.py", line 16, in 
from galaxy.visualization.data_providers.registry import
DataProviderRegistry
  File "/data/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
line 4, in 
from galaxy.visualization.data_providers import genome
  File "/data/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
line 15, in 
from bx.bbi.bigbed_file import BigBedFile
ImportError: No module named bigbed_file


I've already reinstall in galaxy virtual env lot of modules required
as bx-python , pyyaml, pysam, webhelpers...
But it's infinite and I don't understand why all python modules are
not retrieve while the galaxy instance works fine and I've had no
problem when I've updated the galaxy version.

How can I manage this problem and eventually re-install python, python
modules in virtual env ?

Thanks a lot.

Julie
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Re: [galaxy-dev] cleanup datasets error

[Bjoern Gruening]

Wuhu!

On 14.06.2016 11:25, Philipp Rathert wrote:

RE: [galaxy-dev] cleanup datasets error

Hi Bjoern,

Works now.

Thank you very much,

Philipp

*From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
*Sent:* Tuesday, June 14, 2016 11:07 AM
*To:* Rathert, Philipp, Dr. 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] cleanup datasets error

Hi,

can you please do this before executing the script. This will source 
your Galaxy virtual-env.


"""
source $GALAXY_VIRTUAL_ENV/bin/activate
"""

Ciao,
Bjoern


On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote:

Hi Bjoern,



I edited the galaxy.ini directly and started the script.
Unfortunately I get a different error:





Traceback (most recent call last):

File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in


  main()

File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

  app = CleanupDatasetsApplication( config )

File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in
__init__

  self.model = galaxy.model.mapping.init( config.file_path,
config.database_connection, engine_options={},
create_tables=False, object_store=self.object_store )

File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

  engine = build_engine( url, engine_options,
database_query_profiling_proxy, trace_logger )

File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py",
line 20, in build_engine

  engine = create_engine( url, proxy=proxy, **engine_options )

File

"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
line 386, in create_engine

  return strategy.create(*args, **kwargs)

File

"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
line 75, in create

  dbapi = dialect_cls.dbapi(**dbapi_args)

File

"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
line 579, in dbapi

  import psycopg2

ImportError: No module named psycopg2



Can I install the python-psycopq2 module via apt-get in the
container and would this help to fix thee issue?



Cheers,



Philipp



-Original message-
*From:* Rathert, Philipp, Dr.

<mailto:philipp.rath...@ibc.uni-stuttgart.de>
*Sent:* Tuesday 14th June 2016 9:56
*To:* Bjoern Gruening 
<mailto:bjoern.gruen...@gmail.com>
*Cc:* galaxy-dev 
<mailto:galaxy-dev@lists.galaxyproject.org>
*Subject:* Re: [galaxy-dev] cleanup datasets error


Hi Bjoern,

This is wired. It worked before...

I will add this to the galaxy.ini in the config folder and try
again.

Cheers,

Philipp

---Philipp on the road---


Am 14.06.2016 um 09:50 schrieb Bjoern Gruening
mailto:bjoern.gruen...@gmail.com>>:

Hi,

I don't think this will work with the script. This script
reads the config file you specify config/galaxy.ini. And
hence it needs to be added in this file, not via -e variables.
This is probably something we should improve.

Ciao,
Bjoern


> cleanup datasets

error

>

> HI Björn,

>

>

>

> I have added these to the galaxy.ini via
the docker

specific e-

> variables during startup of the container.

>

>

>

> How can I check if they are broken?

>

>

>

> Cheers,

>

>

>

> Philipp

>

>

>

> *From:*Bjoern Gruening
[mailto:bjoern.gruen...@gmail.com]

*Sent:*

> Tuesday, June 14, 2016 9:30 AM *To:*
Rathert,

Philipp, Dr.

> 
<mailto:philipp.rath...@ibc.uni-stuttgart.de>;

galaxy-dev

> 
<mailto:galaxy-dev@lists.galaxyproject.org>

Re: [galaxy-dev] cleanup datasets error

[Philipp Rathert]

Hi Bjoern,

 

Works now. 

Thank you very much,

 

Philipp

 

From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] 
Sent: Tuesday, June 14, 2016 11:07 AM
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] cleanup datasets error

 

Hi,

can you please do this before executing the script. This will source your 
Galaxy virtual-env.

"""
source $GALAXY_VIRTUAL_ENV/bin/activate
"""

Ciao,
Bjoern




On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote:

Hi Bjoern,







I edited the galaxy.ini directly and started the script. Unfortunately I get a 
different error:









Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 

main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__

self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )

  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

engine = build_engine( url, engine_options, database_query_profiling_proxy, 
trace_logger )

  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in 
build_engine

engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
 line 386, in create_engine

return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
 line 75, in create

dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
 line 579, in dbapi

import psycopg2

ImportError: No module named psycopg2





Can I install the python-psycopq2 module via apt-get in the container and would 
this help to fix thee issue?





Cheers,





Philipp





-Original message-
From: Rathert, Philipp, Dr.  <mailto:philipp.rath...@ibc.uni-stuttgart.de> 

Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening  <mailto:bjoern.gruen...@gmail.com> 

Cc: galaxy-dev  <mailto:galaxy-dev@lists.galaxyproject.org> 

Subject: Re: [galaxy-dev] cleanup datasets error




Hi Bjoern,

 

This is wired. It worked before...

I will add this to the galaxy.ini in the config folder and try again.

 

Cheers,

Philipp

---Philipp on the road---


Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >:

Hi,

I don't think this will work with the script. This script reads the config file 
you specify config/galaxy.ini. And hence it needs to be added in this file, not 
via -e variables.
This is probably something we should improve.

Ciao,
Bjoern


> cleanup datasets

error



> 



> HI Björn,



> 



> 



> 



> I have added these to the galaxy.ini via the docker

specific e-



> variables during startup of the container.



> 



> 



> 



> How can I check if they are broken?



> 



> 



> 



> Cheers,



> 



> 



> 



> Philipp



> 



> 



> 



> *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]

*Sent:*



> Tuesday, June 14, 2016 9:30 AM *To:* Rathert,

    Philipp, Dr.



>  <mailto:philipp.rath...@ibc.uni-stuttgart.de> 
;

galaxy-dev



>  <mailto:galaxy-dev@lists.galaxyproject.org> 


*Subject:* Re: [galaxy-dev]



> cleanup datasets error



> 



> 



> 



> Hi Philipp,



> 



> have you followed this from the readme?



> 



> 



> Note that if you would like to run any of the

cleanup scripts



>

 
<https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>
 
<https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,



> you will need to add the following to



   

Re: [galaxy-dev] cleanup datasets error

[Bjoern Gruening]

Hi,

can you please do this before executing the script. This will source 
your Galaxy virtual-env.


"""
source $GALAXY_VIRTUAL_ENV/bin/activate
"""

Ciao,
Bjoern



On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote:

RE: [galaxy-dev] cleanup datasets error

Hi Bjoern,


I edited the galaxy.ini directly and started the script. Unfortunately 
I get a different error:




Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 



main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in 
__init__


self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )


  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

engine = build_engine( url, engine_options, 
database_query_profiling_proxy, trace_logger )


  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 
20, in build_engine


engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py", 
line 386, in create_engine


return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", 
line 75, in create


dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", 
line 579, in dbapi


import psycopg2

ImportError: No module named psycopg2


Can I install the python-psycopq2 module via apt-get in the container 
and would this help to fix thee issue?



Cheers,


Philipp


-Original message-
*From:* Rathert, Philipp, Dr. 
*Sent:* Tuesday 14th June 2016 9:56
*To:* Bjoern Gruening 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] cleanup datasets error

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening
mailto:bjoern.gruen...@gmail.com>>:


Hi,

I don't think this will work with the script. This script reads
the config file you specify config/galaxy.ini. And hence it needs
to be added in this file, not via -e variables.
This is probably something we should improve.

Ciao,
Bjoern


> cleanup datasets error
>
> HI Björn,
>
>
>
> I have added these to the galaxy.ini via the docker specific e-
> variables during startup of the container.
>
>
>
> How can I check if they are broken?
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>
> *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
> Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
> ; galaxy-dev
>  *Subject:* Re: [galaxy-dev]
> cleanup datasets error
>
>
>
> Hi Philipp,
>
> have you followed this from the readme?
>
>
> Note that if you would like to run any of the cleanup scripts
>

<https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,
> you will need to add the following to
> |/export/galaxy-central/config/galaxy.ini|:
>
> |database_connection =
> postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
> /export/galaxy-central/database/files|
>
> Or is this broken? Cheers, Bjoern
>
> On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
>
> Dear all,
>
>
>
> when I want to start the cleanup datasets script I get the
following
> error.
>
>
>
> (.venv)root@galaxy:/galaxy-central# python
> /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
> config/galaxy.ini -d -10 -1
>
> Traceback (most recent call last):
>
> File
"/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 544, in 
>
> main()
>
> File
"/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 99, in main
>
> for key, value in config_parser.items( "app:main" ):
>
> File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
>
> raise NoSectionError(section)
>
> ConfigPar

Re: [galaxy-dev] cleanup datasets error

[Rathert , Philipp , Dr .]

Hi Bjoern,



I edited the galaxy.ini directly and started the script. Unfortunately I get a 
different error:





Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 

    main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

    app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__

    self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )

  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

    engine = build_engine( url, engine_options, database_query_profiling_proxy, 
trace_logger )

  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in 
build_engine

    engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
 line 386, in create_engine

    return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
 line 75, in create

    dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
 line 579, in dbapi

    import psycopg2

ImportError: No module named psycopg2



Can I install the python-psycopq2 module via apt-get in the container and would 
this help to fix thee issue?



Cheers,



Philipp



-Original message-
From: Rathert, Philipp, Dr. 
Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] cleanup datasets error

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > ; galaxy-dev
 >  *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 ><https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in 
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > 
 > 
 > -Original message- *From:* Marius van den Beek
 >  <mailto:m.vandenb...@gmail.com> *Sent:*
 > Tuesday 7th Ju

Re: [galaxy-dev] cleanup datasets error

[Rathert , Philipp , Dr .]

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > ; galaxy-dev
 >  *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 ><https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in 
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > 
 > 
 > -Original message- *From:* Marius van den Beek
 >  <mailto:m.vandenb...@gmail.com> *Sent:*
 > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
 >  <mailto:ma.tang...@gmail.com> *Cc:* galaxy-dev
 > 
 > <mailto:galaxy-dev@lists.galaxyproject.org> *Subject:* Re:
 > [galaxy-dev] Python tool wrapper with multiple input and output
 > files
 > 
 > 
 > Hi Marco,
 > 
 > 
 > 
 > you've got an interesting use-case there.
 > 
 > You may want to use either a dataset list (if you only supply
 > rna_n.bam),
 > 
 > or a paired dataset list (rna_n.bam and dna_n.bam).
 > 
 > I would probably implement a conditional, where the user selects
 > either a dataset list or a paired dataset list.
 > 
 > The output would then be another collection of output files.
 > 
 > Have a look at the test tool folder, and see if any of the tools
 > named collection_*.xml fits what you would like to do
 > 
 > https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
 >
 >
 > 
 These two may be a good basis for what you want to achieve:
 > 
 >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
 >
 >
 > 
 [this one creates an output collection]
 > 
 >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
 >
 >
 > 
 [this one has a conditional to either select a list or a paired list as input]
 > 
 > 
 > 
 > Let us know if you need more help!
 > 
 > 
 > 
 > Cheers,
 > 
 > Marius
 > 
 > 
 > 
 > On 7 June 2016 at 09:50, Marco Tangaro  <mailto:ma.tang...@gmail.com>> wrote:
 > 
 > Dear experts, my name is Marco and I'm working to port our python
 > tool to the Galaxy framework. The main script needs a rna.bam file as
 > input, a reference fasta file, both mandatory. Finally,

Re: [galaxy-dev] cleanup datasets error

[Bjoern Gruening]

Hi,

I don't think this will work with the script. This script reads the 
config file you specify config/galaxy.ini. And hence it needs to be 
added in this file, not via -e variables.

This is probably something we should improve.

Ciao,
Bjoern



cleanup datasets error

>
> HI Björn,
>
>
>
> I have added these to the galaxy.ini via the docker specific e-
> variables during startup of the container.
>
>
>
> How can I check if they are broken?
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>
> *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
> Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
> ; galaxy-dev
>  *Subject:* Re: [galaxy-dev]
> cleanup datasets error
>
>
>
> Hi Philipp,
>
> have you followed this from the readme?
>
>
> Note that if you would like to run any of the cleanup scripts
> 
<https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,

> you will need to add the following to
> |/export/galaxy-central/config/galaxy.ini|:
>
> |database_connection =
> postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
> /export/galaxy-central/database/files|
>
> Or is this broken? Cheers, Bjoern
>
> On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
>
> Dear all,
>
>
>
> when I want to start the cleanup datasets script I get the following
> error.
>
>
>
> (.venv)root@galaxy:/galaxy-central# python
> /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
> config/galaxy.ini -d -10 -1
>
> Traceback (most recent call last):
>
> File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 544, in 
>
> main()
>
> File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
> line 99, in main
>
> for key, value in config_parser.items( "app:main" ):
>
> File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
>
> raise NoSectionError(section)
>
> ConfigParser.NoSectionError: No section: 'app:main'
>
>
>
>
>
> We are using the docker galaxy stable 16.04 version. Before this
> script always worked without producing any error.
>
>
>
> It would be great if anybody has an idea how to fix this...
>
>
>
> Thank you very much in advance.
>
>
>
> Cheers,
>
>
>
> Philipp
>
>
>
>
>
> -Original message- *From:* Marius van den Beek
>  <mailto:m.vandenb...@gmail.com> *Sent:*
> Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
>  <mailto:ma.tang...@gmail.com> *Cc:* galaxy-dev
> 
> <mailto:galaxy-dev@lists.galaxyproject.org> *Subject:* Re:
> [galaxy-dev] Python tool wrapper with multiple input and output
> files
>
>
> Hi Marco,
>
>
>
> you've got an interesting use-case there.
>
> You may want to use either a dataset list (if you only supply
> rna_n.bam),
>
> or a paired dataset list (rna_n.bam and dna_n.bam).
>
> I would probably implement a conditional, where the user selects
> either a dataset list or a paired dataset list.
>
> The output would then be another collection of output files.
>
> Have a look at the test tool folder, and see if any of the tools
> named collection_*.xml fits what you would like to do
>
> https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
>
>
>
These two may be a good basis for what you want to achieve:


> 
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml

>
>
>
[this one creates an output collection]


> 
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml

>
>
>
[this one has a conditional to either select a list or a paired list as 
input]



>
>
> Let us know if you need more help!
>
>
>
> Cheers,
>
> Marius
>
>
>
> On 7 June 2016 at 09:50, Marco Tangaro  <mailto:ma.tang...@gmail.com>> wrote:
>
> Dear experts, my name is Marco and I'm working to port our python
> tool to the Galaxy framework. The main script needs a rna.bam file as
> input, a reference fasta file, both mandatory. Finally, you can add a
> dna.bam file, but this is optional. Therefore an example command is:
>
> script.py -i rna.bam -f reference.fa -j dna.bam
>
> The outout is a tabular. Again the -j dna.bam option is completely
> optional. So quite soon it turned out that I had to use a python
> wrapper to parse our script. Now the wrapper works fine.
>
>
> The next step is to run the tool over multiple input file and we
> would like to avoid to use a workflow.
>
> The idea is that to each in

Re: [galaxy-dev] cleanup datasets error

[Philipp Rathert]

HI Björn,

 

I have added these to the galaxy.ini via the docker specific e- variables 
during startup of the container.

 

How can I check if they are broken?

 

Cheers,

 

Philipp

 

From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] 
Sent: Tuesday, June 14, 2016 9:30 AM
To: Rathert, Philipp, Dr. ; galaxy-dev 

Subject: Re: [galaxy-dev] cleanup datasets error

 

Hi Philipp,

have you followed this from the readme?




Note that if you would like to run any of the  
<https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>
 cleanup scripts, you will need to add the following to 
/export/galaxy-central/config/galaxy.ini:

database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files

Or is this broken?
Cheers,
Bjoern



On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:

Dear all,







when I want to start the cleanup datasets script I get the following error.





(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'









We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 







It would be great if anybody has an idea how to fix this...





Thank you very much in advance.





Cheers,





Philipp 









-Original message-
From: Marius van den Beek  <mailto:m.vandenb...@gmail.com> 

Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro  <mailto:ma.tang...@gmail.com> 
Cc: galaxy-dev  <mailto:galaxy-dev@lists.galaxyproject.org> 

Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and output 
files




Hi Marco, 

 

you've got an interesting use-case there.

You may want to use either a dataset list (if you only supply rna_n.bam),

or a paired dataset list (rna_n.bam and dna_n.bam). 

I would probably implement a conditional, where the user selects either a 
dataset list or a paired dataset list.

The output would then be another collection of output files.

Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do

https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools

These two may be a good basis for what you want to achieve:

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml

[this one creates an output collection]

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml

[this one has a conditional to either select a list or a paired list as input]

 

Let us know if you need more help!

 

Cheers,

Marius

 

On 7 June 2016 at 09:50, Marco Tangaro mailto:ma.tang...@gmail.com> > wrote:

Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, both 
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our 
script. Now the wrapper works fine.


The next step is to run the tool over multiple input file and we would like to 
avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference 
is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they 
correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to 
the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco


___
Please keep all replies on the list by using "reply all"
in your mail client. 

Re: [galaxy-dev] cleanup datasets error

[Bjoern Gruening]

Hi Philipp,

have you followed this from the readme?

Note that if you would like to run any of thecleanup scripts 
, 
you will need to add the following 
to|/export/galaxy-central/config/galaxy.ini|:


|database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files|

Or is this broken?
Cheers,
Bjoern


On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:

cleanup datasets error

Dear all,


when I want to start the cleanup datasets script I get the following 
error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py 
config/galaxy.ini -d -10 -1


Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", 
line 544, in 


main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", 
line 99, in main


for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'



We are using the docker galaxy stable 16.04 version. Before this 
script always worked without producing any error.



It would be great if anybody has an idea how to fix this...


Thank you very much in advance.


Cheers,


Philipp



-Original message-
*From:* Marius van den Beek 
*Sent:* Tuesday 7th June 2016 14:06
*To:* Marco Tangaro 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] Python tool wrapper with multiple input 
and output files


Hi Marco,

you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam).
I would probably implement a conditional, where the user selects 
either a dataset list or a paired dataset list.

The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do

https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
These two may be a good basis for what you want to achieve:
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
[this one creates an output collection]
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
[this one has a conditional to either select a list or a paired list 
as input]


Let us know if you need more help!

Cheers,
Marius

On 7 June 2016 at 09:50, Marco Tangaro > wrote:

Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, 
both mandatory. Finally, you can add a dna.bam file, but this is optional.

Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to 
parse our script. Now the wrapper works fine.



The next step is to run the tool over multiple input file and we would 
like to avoid to use a workflow.


The idea is that to each input file corresponds an output file. The 
reference is still the same.

For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple 
input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, 
that they correspond to the right rna_xyz.bam file.


I would like to have as output a page which is showing as results the 
link to the single output files as suggested here.

https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco

___
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/

[galaxy-dev] cleanup datasets error

[Rathert , Philipp , Dr .]

Dear all,



when I want to start the cleanup datasets script I get the following error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

    main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

    for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

    raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'






We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 



It would be great if anybody has an idea how to fix this...



Thank you very much in advance.



Cheers,



Philipp 





-Original message-
From: Marius van den Beek 
Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and 
outputfiles


Hi Marco,

you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam). 
I would probably implement a conditional, where the user selects either a 
dataset list or a paired dataset list.
The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do
https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
These two may be a good basis for what you want to achieve:
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
[this one creates an output collection]
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
[this one has a conditional to either select a list or a paired list as input]

Let us know if you need more help!

Cheers,
Marius

On 7 June 2016 at 09:50, Marco Tangaro mailto:ma.tang...@gmail.com> > wrote:
Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, both 
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our 
script. Now the wrapper works fine.


The next step is to run the tool over multiple input file and we would like to 
avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference 
is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they 
correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to 
the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco

___
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/

Re: [galaxy-dev] cleanup

[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
 >>  > versio

Re: [galaxy-dev] cleanup

[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 <mailto:nsora...@tiscali.it>>:



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. 
<mailto:philipp.rath...@ibc.uni-stuttgart.de>>;
>> galaxy-dev@lists.galaxyproject.org 
<mailto: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
>>  >
>>  > --
>>  >
&

Re: [galaxy-dev] cleanup

[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
 > <mailto: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

[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
 > <mailto: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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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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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] cleanup

[Hans-Rudolf Hotz]

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



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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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[galaxy-dev] cleanup

[Philipp Rathert]

Dear All,

 

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. 

 

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

 

 

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

 

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in your mail client.  To manage your subscriptions to this
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