Re: [galaxy-dev] cleanup datasets error
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
___________________________________________________________ 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:
___________________________________________________________ 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, 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:
RE: [galaxy-dev] cleanup datasets error
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 > > > ___________________________________________________________ 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/ > > >
___________________________________________________________
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, Works now. Thank you very much, Philipp From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] Sent: Tuesday, June 14, 2016 11:07 AM To: Rathert, Philipp, Dr. <philipp.rathert@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. <mailto:philipp.rathert@ibc.uni-stuttgart.de> <philipp.rathert@ibc.uni-stuttgart.de> Sent: Tuesday 14th June 2016 9:56 To: Bjoern Gruening <mailto:bjoern.gruening@gmail.com> <bjoern.gruening@gmail.com> Cc: galaxy-dev <mailto:galaxy-dev@lists.galaxyproject.org> <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. > <mailto:philipp.rathert@ibc.uni-stuttgart.de> <philipp.rathert@ibc.uni-stuttgart.de>; galaxy-dev > <mailto:galaxy-dev@lists.galaxyproject.org> <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 > <mailto:m.vandenbeek@gmail.com> <m.vandenbeek@gmail.com> <mailto:m.vandenbeek@gmail.com> <mailto:m.vandenbeek@gmail.com> *Sent:* > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro > <mailto:ma.tangaro@gmail.com> <ma.tangaro@gmail.com> <mailto:ma.tangaro@gmail.com> <mailto:ma.tangaro@gmail.com> *Cc:* galaxy-dev > <mailto:galaxy-dev@lists.galaxyproject.org> <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/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> > <mailto: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/ > > > ___________________________________________________________ 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/
Wuhu! On 14.06.2016 11:25, Philipp Rathert wrote:
RE: [galaxy-dev] cleanup datasets error
Hi Bjoern,
Works now.
Thank you very much,
Philipp
*From:*Bjoern Gruening [mailto:bjoern.gruening@gmail.com] *Sent:* Tuesday, June 14, 2016 11:07 AM *To:* Rathert, Philipp, Dr. <philipp.rathert@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.rathert@ibc.uni-stuttgart.de> <mailto:philipp.rathert@ibc.uni-stuttgart.de> *Sent:* Tuesday 14th June 2016 9:56 *To:* Bjoern Gruening <bjoern.gruening@gmail.com> <mailto:bjoern.gruening@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.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> <mailto:philipp.rathert@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.vandenbeek@gmail.com> <mailto:m.vandenbeek@gmail.com>
<mailto: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>
<mailto:ma.tangaro@gmail.com> <mailto:ma.tangaro@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/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>
> <mailto: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/
>
>
>
___________________________________________________________
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.