Re: [galaxy-dev] tool development

2016-01-19 Thread Hans-Rudolf Hotz 

Hi Matthias

Have you considered "Data Libraries"?

A cron job can query your LIMS and use the API to create "Data 
Libraries". Then the user can select which datasets she/he wants to import.



And back to your original question: Yes, it is possible to create 
interactive tools. Check out the 'dynamic_options' examples on


https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax


Regards, Hans-Rudolf

On 01/19/2016 12:18 PM, Matthias De Smet wrote:

Hi All,

I would like to create a tool to import data from a sequencer on a networked 
share to a users history.
The ideal setup would be that a query can be submitted to a database which 
contains all metadata from the sequencer + the path of the sequencer output. 
The tool should then show the available datasets found in the database and 
provide checkboxes to select which data should be imported.

My question is: how do you guys propose I get started on this? Do I use the 
API? Is it even possible to get a tool to return some output without submitting 
it as a job, e.g. using it interactively?

Thanks for the help!

PS: I know the basics of tool development, but I haven’t got much experience, 
so all comments are welcome!

Matthias
___
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/

Re: [galaxy-dev] tool development

2016-01-19 Thread Matthias De Smet 
Hi Hans-Rudolf

Yes, we have considered using data libraries, but for this particular use case 
we would prefer an approach like this. Our users are notoriously bad at data 
management and we would like to limit the amount of data that gets loaded in 
Galaxy. The networked share does not store all data permanently, so we need 
something to query what is available so the users can load that into their 
history.

Ideally the datasets also shouldn’t be copied into Galaxy, but symlinked, if 
possible.

Thanks for the tip on ‘dynamic_options’. Hadn’t noticed it before.

Matthias


> Op 19 jan. 2016, om 13:40 heeft Hans-Rudolf Hotz  het volgende 
> geschreven:
> 
> Hi Matthias
> 
> Have you considered "Data Libraries"?
> 
> A cron job can query your LIMS and use the API to create "Data Libraries". 
> Then the user can select which datasets she/he wants to import.
> 
> 
> And back to your original question: Yes, it is possible to create interactive 
> tools. Check out the 'dynamic_options' examples on
> 
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
> 
> 
> Regards, Hans-Rudolf
> 
> On 01/19/2016 12:18 PM, Matthias De Smet wrote:
>> Hi All,
>> 
>> I would like to create a tool to import data from a sequencer on a networked 
>> share to a users history.
>> The ideal setup would be that a query can be submitted to a database which 
>> contains all metadata from the sequencer + the path of the sequencer output. 
>> The tool should then show the available datasets found in the database and 
>> provide checkboxes to select which data should be imported.
>> 
>> My question is: how do you guys propose I get started on this? Do I use the 
>> API? Is it even possible to get a tool to return some output without 
>> submitting it as a job, e.g. using it interactively?
>> 
>> Thanks for the help!
>> 
>> PS: I know the basics of tool development, but I haven’t got much 
>> experience, so all comments are welcome!
>> 
>> Matthias
>> ___
>> 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/

Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.

2015-01-26 Thread John Chilton 
I have created a Trello card to track this request here
https://trello.com/c/qCtBBB8n.

Any chance you can share the tool with me? I understand that this
instinct is too simplistic - but it seems to me like the option to
repeatedly run a tool over many datasets should not be the concern of
the tool author - it is a user concern. If we add the option - perhaps
we could stipulate that it requests some other parameter to dependent
on it (I assume you have a dependent parameter in the repeat?).

-John

On Thu, Jan 22, 2015 at 5:50 AM, Vimalkumar Velayudhan
vi...@biotechcoder.com wrote:
 Thanks Peter. I see how this feature would be useful, but the program I'm
 writing a wrapper for has an argument with values corresponding to the input
 files. I am using a repeat tag to maintain this order. With the multi-run
 option, files are selected in a random manner and added to the job queue. It
 is best not to display the multi-run option in this case.

 I see there is a TODO on this already:
 https://bitbucket.org/galaxy/galaxy-dist/src/a2308bdc93b897af974766b190abe019ade49e9a/lib/galaxy/tools/parameters/basic.py?at=default#cl-2084

 For now, I have set allow=False but I believe this is best set at the param
 tag level:

 param type=data multirun=false /


 Vimal

 On Wed, Jan 21, 2015 at 2:26 AM, Peter Cock p.j.a.c...@googlemail.com
 wrote:

 I think this is the (relatively new) Galaxy ability to automatically
 run N copies of your tool given N input files, making N outputs
 and is related to the collections work.

 (This is possible if your tool takes a single input file)

 Peter

 On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan
 vi...@biotechcoder.com wrote:
  Hi all,
 
  I am trying to create a select box with the possibility of selecting
  only a
  single item from the input dataset (figure 1). This works fine but the
  option for selecting multiple files is still visible (figure 2). The
  multiple=false attribute has no effect.
 
  Figure: http://i.imgur.com/oJVFCoF.png
 
  I have the following in my XML.
 
  param format=tabular name=ribo_files type=data
 label=Select Ribo-Seq alignment file multiple=false 
  /param
 
  Any suggestions?
 
  galaxy-dist revision 5f4c13d622b8
 
 
  Regards,
  Vimalkumar Velayudhan
 
  ___
  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/

Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.

2015-01-22 Thread Vimalkumar Velayudhan 
Thanks Peter. I see how this feature would be useful, but the program I'm
writing a wrapper for has an argument with values corresponding to the
input files. I am using a repeat tag to maintain this order. With the
multi-run option, files are selected in a random manner and added to the
job queue. It is best not to display the multi-run option in this case.

I see there is a TODO on this already:
https://bitbucket.org/galaxy/galaxy-dist/src/a2308bdc93b897af974766b190abe019ade49e9a/lib/galaxy/tools/parameters/basic.py?at=default#cl-2084

For now, I have set allow=False but I believe this is best set at the param
tag level:

param type=data multirun=false /


Vimal

On Wed, Jan 21, 2015 at 2:26 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 I think this is the (relatively new) Galaxy ability to automatically
 run N copies of your tool given N input files, making N outputs
 and is related to the collections work.

 (This is possible if your tool takes a single input file)

 Peter

 On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan
 vi...@biotechcoder.com wrote:
  Hi all,
 
  I am trying to create a select box with the possibility of selecting
 only a
  single item from the input dataset (figure 1). This works fine but the
  option for selecting multiple files is still visible (figure 2). The
  multiple=false attribute has no effect.
 
  Figure: http://i.imgur.com/oJVFCoF.png
 
  I have the following in my XML.
 
  param format=tabular name=ribo_files type=data
 label=Select Ribo-Seq alignment file multiple=false 
  /param
 
  Any suggestions?
 
  galaxy-dist revision 5f4c13d622b8
 
 
  Regards,
  Vimalkumar Velayudhan
 
  ___
  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/

Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.

2015-01-20 Thread Peter Cock 
I think this is the (relatively new) Galaxy ability to automatically
run N copies of your tool given N input files, making N outputs
and is related to the collections work.

(This is possible if your tool takes a single input file)

Peter

On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan
vi...@biotechcoder.com wrote:
 Hi all,

 I am trying to create a select box with the possibility of selecting only a
 single item from the input dataset (figure 1). This works fine but the
 option for selecting multiple files is still visible (figure 2). The
 multiple=false attribute has no effect.

 Figure: http://i.imgur.com/oJVFCoF.png

 I have the following in my XML.

 param format=tabular name=ribo_files type=data
label=Select Ribo-Seq alignment file multiple=false 
 /param

 Any suggestions?

 galaxy-dist revision 5f4c13d622b8


 Regards,
 Vimalkumar Velayudhan

 ___
 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/

Re: [galaxy-dev] Tool Development DELLY

2015-01-12 Thread Peter Cock 
Hi Marco,

No problem - I originally copied the metadata access
trick from one of the Galaxy dev-team's tool anyway.

Maybe we need to add this to the wiki...

Peter

On Tuesday, January 13, 2015, Marco Albuquerque 
marcoalbuquerque@gmail.com wrote:

 Hi Peter,

 I was unaware of how to access metadata, that seemed to be my issue. The
 tool works now though!

 Thanks so much,

 Marco




 On 2015-01-09 7:13 PM, Peter Cock p.j.a.c...@googlemail.com
 javascript:; wrote:
 
 I think the symlink approach is best, see for example the Python
 wrapper script I used here for samtools idxstats,
 
 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
 
 However, you can make the link in the XML directly, see Dave's
 reworking of this wrapper:
 
 https://github.com/galaxyproject/tools-devteam/tree/master/tool_collection
 s/samtools/samtools_idxstats
 
 Regards,
 
 Peter



___
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/