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>:

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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