[galaxy-dev] Multiple output datasets
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 ___ 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/
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 [1]martinchristianse...@hotmail.com To: [2]galaxy-dev@lists.bx.psu.edu [3]galaxy-dev@lists.bx.psu.edu 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: [4]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: [5]http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: [6]http://galaxyproject.org/search/mailinglists/ References 1. mailto:martinchristianse...@hotmail.com 2. mailto:galaxy-dev@lists.bx.psu.edu 3. mailto:galaxy-dev@lists.bx.psu.edu 4. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files. 5. http://lists.bx.psu.edu/ 6. 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/
Re: [galaxy-dev] Multiple output datasets
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: stefvanliesh...@fastmail.fm To: galaxy-dev@lists.bx.psu.edu 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 martinchristianse...@hotmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 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: 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/ ___ 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/
Re: [galaxy-dev] Multiple output datasets
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 [1]martinchristianse...@hotmail.com To: Stef van Lieshout [2]stefvanliesh...@fastmail.fm, [3]galaxy-dev@lists.bx.psu.edu [4]galaxy-dev@lists.bx.psu.edu 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 __ From: stefvanliesh...@fastmail.fm To: galaxy-dev@lists.bx.psu.edu 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 [5]martinchristianse...@hotmail.com To: [6]galaxy-dev@lists.bx.psu.edu [7]galaxy-dev@lists.bx.psu.edu 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: [8]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: [9]http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: [10]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/ References 1. mailto:martinchristianse...@hotmail.com 2. mailto:stefvanliesh...@fastmail.fm 3. mailto:galaxy-dev@lists.bx.psu.edu 4. mailto:galaxy-dev@lists.bx.psu.edu 5. mailto:martinchristianse...@hotmail.com 6. mailto:galaxy-dev@lists.bx.psu.edu 7. mailto:galaxy-dev@lists.bx.psu.edu 8. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files. 9. http://lists.bx.psu.edu/ 10. 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/
Re: [galaxy-dev] Multiple output datasets
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: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 martinchristianse...@hotmail.com To: Stef van Lieshout stefvanliesh...@fastmail.fm, galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 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 From: stefvanliesh...@fastmail.fm To: galaxy-dev@lists.bx.psu.edu 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 martinchristianse...@hotmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 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: 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/ ___ 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/
Re: [galaxy-dev] Multiple output datasets
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 [1]martinchristianse...@hotmail.com To: Stef van Lieshout [2]stefvanliesh...@fastmail.fm, [3]galaxy-dev@lists.bx.psu.edu [4]galaxy-dev@lists.bx.psu.edu 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 __ From: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 [5]martinchristianse...@hotmail.com To: Stef van Lieshout [6]stefvanliesh...@fastmail.fm, [7]galaxy-dev@lists.bx.psu.edu [8]galaxy-dev@lists.bx.psu.edu 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 __ From: stefvanliesh...@fastmail.fm To: galaxy-dev@lists.bx.psu.edu 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 [9]martinchristianse...@hotmail.com To: [10]galaxy-dev@lists.bx.psu.edu [11]galaxy-dev@lists.bx.psu.edu 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: [12]https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Outpu t%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: [13]http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: [14]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/ References 1. mailto:martinchristianse...@hotmail.com 2. mailto:stefvanliesh...@fastmail.fm 3. mailto:galaxy-dev@lists.bx.psu.edu 4. mailto:galaxy-dev@lists.bx.psu.edu 5. mailto:martinchristianse...@hotmail.com 6. mailto:stefvanliesh...@fastmail.fm 7. mailto:galaxy-dev@lists.bx.psu.edu 8. mailto:galaxy-dev@lists.bx.psu.edu 9. mailto:martinchristianse...@hotmail.com 10. mailto:galaxy-dev@lists.bx.psu.edu 11. mailto:galaxy-dev@lists.bx.psu.edu 12. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files. 13. http://lists.bx.psu.edu/ 14
Re: [galaxy-dev] Multiple output datasets
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: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 martinchristianse...@hotmail.com To: Stef van Lieshout stefvanliesh...@fastmail.fm, galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 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 From: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 martinchristianse...@hotmail.com To: Stef van Lieshout stefvanliesh...@fastmail.fm, galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 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 From: stefvanliesh...@fastmail.fm To: galaxy-dev@lists.bx.psu.edu 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 martinchristianse...@hotmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 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: 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/ ___ 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
Re: [galaxy-dev] Multiple output datasets
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 [1]martinchristianse...@hotmail.com To: Stef van Lieshout [2]stefvanliesh...@fastmail.fm, [3]galaxy-dev@lists.bx.psu.edu [4]galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Multiple output datasets Date: Wed, 27 Aug 2014 16:25:07 +0200 But where are the variables defined then? Martin __ From: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 [5]martinchristianse...@hotmail.com To: Stef van Lieshout [6]stefvanliesh...@fastmail.fm, [7]galaxy-dev@lists.bx.psu.edu [8]galaxy-dev@lists.bx.psu.edu 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 __ From: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 [9]martinchristianse...@hotmail.com To: Stef van Lieshout [10]stefvanliesh...@fastmail.fm, [11]galaxy-dev@lists.bx.psu.edu [12]galaxy-dev@lists.bx.psu.edu 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 __ From: stefvanliesh...@fastmail.fm To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu 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 [13]martinchristianse...@hotmail.com To: Stef van Lieshout [14]stefvanliesh...@fastmail.fm, [15]galaxy-dev@lists.bx.psu.edu [16]galaxy-dev@lists.bx.psu.edu 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 __ From: stefvanliesh...@fastmail.fm To: galaxy-dev@lists.bx.psu.edu 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 [17]martinchristianse...@hotmail.com To: [18]galaxy-dev@lists.bx.psu.edu [19]galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Multiple output datasets Date: Wed, 27 Aug 2014 12:04:46
