cleanup datasets error
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> Sent: Tuesday 7th June 2016 14:06 To: Marco Tangaro <ma.tangaro@gmail.com> Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and outputfiles 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 ___________________________________________________________ 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/ <http://galaxyproject.org/search/mailinglists/>
Hi Philipp, have you followed this from the readme? Note that if you would like to run any of thecleanup 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:
cleanup datasets error
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> *Sent:* Tuesday 7th June 2016 14:06 *To:* Marco Tangaro <ma.tangaro@gmail.com> *Cc:* galaxy-dev <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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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 <https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets> cleanup scripts, 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 <mailto:m.vandenbeek@gmail.com> <m.vandenbeek@gmail.com> Sent: Tuesday 7th June 2016 14:06 To: Marco Tangaro <mailto:ma.tangaro@gmail.com> <ma.tangaro@gmail.com> Cc: galaxy-dev <mailto:galaxy-dev@lists.galaxyproject.org> <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 ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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
___________________________________________________________ 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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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
___________________________________________________________ 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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
participants (3)
-
Bjoern Gruening -
Philipp Rathert -
Rathert, Philipp, Dr.