Multiple output datasets

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Multiple output datasets

Martin Christiansen
Hi all,

I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.

As I understand, the $__new_file_path__ option is changed in the universe_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.

Any ideas?

Best,
Martin Christiansen

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Re: Multiple output datasets

Stef van Lieshout
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
To search Galaxy mailing lists use the unified search at:

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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Multiple output datasets

Martin Christiansen
Hi Stef,

I always restart galaxy and have done the other parts correct as well, but with no luck.

In my universe_wsgi.ini file I have:

new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory

Does this look familiar?

Martin


From: [hidden email]
To: [hidden email]
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets

It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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Re: Multiple output datasets

Stef van Lieshout
I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
 

___________________________________________________________
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and other Galaxy lists, please use the interface at:
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Re: Multiple output datasets

Martin Christiansen
I went back to not using the options in the .ini file, but it still doesn't work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml command line?

Martin


From: [hidden email]
To: [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:17:13 +0200

I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ 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:
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Re: Multiple output datasets

Stef van Lieshout
In the example they provide it to the sh tool:
<command>
example_tool.sh $input1 $output1 $output1.id $__new_file_path__
</command>
 
...so then the 3rd and 4th variables given to example_tool.sh contain the <id> and the output directory path. Save all the extra output files to that directory with the exact format: primary_<id>_somename_visible_filetype (eg primary_546_output2_visible_bed)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:52:03 +0200
 
I went back to not using the options in the .ini file, but it still doesn't work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml command line?
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:17:13 +0200
 
I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ 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:
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Re: Multiple output datasets

Martin Christiansen
It still doesn't work. I see the files in the folder, but they don't show in galaxy.
My command line looks like this:
myTool.sh $input1 $output1 $output2 546 /my/file/path/

Martin


From: [hidden email]
To: [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:07:52 +0200

In the example they provide it to the sh tool:
<command>
example_tool.sh $input1 $output1 $output1.id $__new_file_path__
</command>
 
...so then the 3rd and 4th variables given to example_tool.sh contain the <id> and the output directory path. Save all the extra output files to that directory with the exact format: primary_<id>_somename_visible_filetype (eg primary_546_output2_visible_bed)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:52:03 +0200
 
I went back to not using the options in the .ini file, but it still doesn't work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml command line?
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:17:13 +0200
 
I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: Multiple output datasets

Stef van Lieshout
Dont use "$output2", "546" and "/my/file/path/".
 
Do exactly this: myTool.sh $input1 $output1 $output1.id $__new_file_path__
 
And then use the variables in your script ("$output.id" will provide you with eg "546" and "$__new_file_path__" with the output path)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:50:26 +0200
 
It still doesn't work. I see the files in the folder, but they don't show in galaxy.
My command line looks like this:
myTool.sh $input1 $output1 $output2 546 /my/file/path/
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:07:52 +0200
 
In the example they provide it to the sh tool:
<command>
example_tool.sh $input1 $output1 $output1.id $__new_file_path__
</command>
 
...so then the 3rd and 4th variables given to example_tool.sh contain the <id> and the output directory path. Save all the extra output files to that directory with the exact format: primary_<id>_somename_visible_filetype (eg primary_546_output2_visible_bed)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:52:03 +0200
 
I went back to not using the options in the .ini file, but it still doesn't work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml command line?
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:17:13 +0200
 
I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: Multiple output datasets

Martin Christiansen
But where are the variables defined then?

Martin


From: [hidden email]
To: [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 16:11:49 +0200

Dont use "$output2", "546" and "/my/file/path/".
 
Do exactly this: myTool.sh $input1 $output1 $output1.id $__new_file_path__
 
And then use the variables in your script ("$output.id" will provide you with eg "546" and "$__new_file_path__" with the output path)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:50:26 +0200
 
It still doesn't work. I see the files in the folder, but they don't show in galaxy.
My command line looks like this:
myTool.sh $input1 $output1 $output2 546 /my/file/path/
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:07:52 +0200
 
In the example they provide it to the sh tool:
<command>
example_tool.sh $input1 $output1 $output1.id $__new_file_path__
</command>
 
...so then the 3rd and 4th variables given to example_tool.sh contain the <id> and the output directory path. Save all the extra output files to that directory with the exact format: primary_<id>_somename_visible_filetype (eg primary_546_output2_visible_bed)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:52:03 +0200
 
I went back to not using the options in the .ini file, but it still doesn't work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml command line?
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:17:13 +0200
 
I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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Re: Multiple output datasets

Stef van Lieshout
I guess that...
 
$output1 you have (hopefully) defined in your <outputs> section, and with ".id" you get the internal galaxy id of that object.
 
And $__new_file_path__ is created by galaxy at execution of the tool.
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 16:25:07 +0200
 
But where are the variables defined then?
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 16:11:49 +0200
 
Dont use "$output2", "546" and "/my/file/path/".
 
Do exactly this: myTool.sh $input1 $output1 $output1.id $__new_file_path__
 
And then use the variables in your script ("$output.id" will provide you with eg "546" and "$__new_file_path__" with the output path)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:50:26 +0200
 
It still doesn't work. I see the files in the folder, but they don't show in galaxy.
My command line looks like this:
myTool.sh $input1 $output1 $output2 546 /my/file/path/
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 15:07:52 +0200
 
In the example they provide it to the sh tool:
<command>
example_tool.sh $input1 $output1 $output1.id $__new_file_path__
</command>
 
...so then the 3rd and 4th variables given to example_tool.sh contain the <id> and the output directory path. Save all the extra output files to that directory with the exact format: primary_<id>_somename_visible_filetype (eg primary_546_output2_visible_bed)
 
Stef
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:52:03 +0200
 
I went back to not using the options in the .ini file, but it still doesn't work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml command line?
 
Martin
 
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:17:13 +0200
 
I do not use "new_file_path" and "collect_outputs_from" in universe_wsgi.ini
 
In my tool code I directly save to files to:
$__new_file_path__/primary_<id>_somename_visible_filetype
 
As they say on the page:
To use this method at least one output dataset (output1 in our example) must be specified - this dataset will act as the reference for our additional datasets. The new additional datasets must be placed in the directory provided by $__new_file_path__ and named in the form: "%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, dbkey(build) ) Where the '_dbkey' portion of the name is optional.
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
To: Stef van Lieshout <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 14:01:03 +0200
 
Hi Stef,
 
I always restart galaxy and have done the other parts correct as well, but with no luck.
 
In my universe_wsgi.ini file I have:
 
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
 
Does this look familiar?
 
Martin
 
Date: Wed, 27 Aug 2014 12:22:35 +0200
Subject: Re: [galaxy-dev] Multiple output datasets
 
It does works for me if I do exactly as described on that page without using the universe_wsgi.ini option:
 
- I have the "force_history_refresh"
- I follow the exact file-name structure (primary_<id>_somename_visible_filetype)
- I save the files in the dir from passed param $__new_file_path__
 
Can you check if that works? Maybe the change in universe_wsgi.ini isn't picked up correctly... Did you restart galaxy?
 
Stef
 
 
----- Original message -----
From: Martin Christiansen <[hidden email]>
Subject: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 12:04:46 +0200
 
Hi all,
 
I'm implementing a tool for our local galaxy instance which has multiple output datasets.
The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
 
As I understand, the $__new_file_path__ option is changed in theuniverse_wsgi.ini file.
Regardless, the extra files created from the tool does not show in the galaxy history.
 
Any ideas?
 
Best,
Martin Christiansen
___________________________________________________________
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:
 
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: http://lists.bx.psu.edu/ 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/