New subject: cleanup datasets error

14 Jun 2016


      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.rathert@ibc.uni-stuttgart.de
Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening bjoern.gruening@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.gruening@gmail.com mailto:bjoern.gruening@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.gruening@gmail.com] *Sent:*
Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
philipp.rathert@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.vandenbeek@gmail.com mailto:m.vandenbeek@gmail.com *Sent:*
Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
ma.tangaro@gmail.com mailto:ma.tangaro@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/colle...
[this one creates an output collection]
...
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/colle...
[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.tangaro@gmail.com
mailto:ma.tangaro@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
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___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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