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. <philipp.rath...@ibc.uni-stuttgart.de>
Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org>
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 <module>

    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> 
<philipp.rath...@ibc.uni-stuttgart.de>
Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening  <mailto:bjoern.gruen...@gmail.com> 
<bjoern.gruen...@gmail.com>
Cc: galaxy-dev  <mailto:galaxy-dev@lists.galaxyproject.org> 
<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 <bjoern.gruen...@gmail.com 
<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> 
<philipp.rath...@ibc.uni-stuttgart.de>;

                galaxy-dev



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



                > |/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 <module>



                > 



                > main()



                > 



                > File

                "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",



                > line 99, in main



                > 



                > for key, value in config_parser.items(  <app:main> "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> <m.vandenb...@gmail.com>

                 <mailto:m.vandenb...@gmail.com> <mailto:m.vandenb...@gmail.com>

                *Sent:*



                > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro



                >  <mailto:ma.tang...@gmail.com> <ma.tang...@gmail.com>

                 <mailto:ma.tang...@gmail.com> <mailto:ma.tang...@gmail.com>

                *Cc:* galaxy-dev



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



                >  <mailto:galaxy-dev@lists.galaxyproject.org> 
<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 <ma.tang...@gmail.com 
<mailto:ma.tang...@gmail.com> 



                >  <mailto:ma.tang...@gmail.com> <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

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                > please use the interface at: https://lists.galaxyproject.org/



                > 



                > To search Galaxy mailing lists use the unified

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                > 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

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                > 



                > https://lists.galaxyproject.org/



                > 



                > 



                > 



                > To search Galaxy mailing lists use the unified

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                > 



                > http://galaxyproject.org/search/mailinglists/



                > 



                > 



                > 



___________________________________________________________
 
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