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/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.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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>
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