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 <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. <philipp.rath...@ibc.uni-stuttgart.de>
    *Sent:* Tuesday 14th June 2016 9:56
    *To:* Bjoern Gruening <bjoern.gruen...@gmail.com>
    *Cc:* galaxy-dev <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.
    > <philipp.rath...@ibc.uni-stuttgart.de>; galaxy-dev
    > <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>,
    > 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" ):
    >
    > 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
    > <m.vandenb...@gmail.com> <mailto:m.vandenb...@gmail.com> *Sent:*
    > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
    > <ma.tang...@gmail.com> <mailto:ma.tang...@gmail.com> *Cc:*
    galaxy-dev
    > <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>> 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:
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    > https://lists.galaxyproject.org/
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    >
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    >
    > http://galaxyproject.org/search/mailinglists/
    >
    >
    >


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