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