subject:"\[galaxy\-dev\] cleanup datasets error"

Re: [galaxy-dev] cleanup datasets error

2016-06-14 Thread 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

2016-06-14 Thread 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

2016-06-14 Thread 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

2016-06-14 Thread 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

2016-06-14 Thread 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

2016-06-14 Thread 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

2016-06-14 Thread 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

2016-06-14 Thread 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/

[galaxy-dev] cleanup datasets error

2016-06-14 Thread 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 datasets error

Re: [galaxy-dev] cleanup datasets error

Re: [galaxy-dev] cleanup datasets error

Re: [galaxy-dev] cleanup datasets error

Re: [galaxy-dev] cleanup datasets error

Re: [galaxy-dev] cleanup datasets error

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Re: [galaxy-dev] cleanup datasets error

[galaxy-dev] cleanup datasets error

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