processing multiple files

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

processing multiple files

mark.rose

Hello

 

Is there a approved way to configure or otherwise use galaxy to process multiple files with a tool or workflow?  Using FASTQ Groomer on dozens of files individually is excruciating.

Thanks

 

Mark




This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/
Reply | Threaded
Open this post in threaded view
|

Re: processing multiple files

Jen Hillman-Jackson
Hi Mark,

Use a workflow to make this simpler. Put as many steps that are redundant into the workflow then add an "Input" dataset to the beginning (this is the important part). In the workflow editor, the "input" dataset is located in tool list (left column), near the bottom.

Then, when bringing up the workflow to run it, there will be a little multi-paged icon next the input dataset's label. See the png here:

           


After choosing inputs, down the page where you click to execute the workflow there is checkbox option to send the results to a new history. This can come in handy sometimes when running on multiple dataset inputs, since it will sort the output into distinct histories for you. Not always wanted, but good to know about.

Hopefully this helps,

Jen
Galaxy team

Look for more here in the upcoming week: https://wiki.galaxyproject.org/Learn/AdvancedWorkflow


On 2/26/14 3:30 PM, [hidden email] wrote:

Hello

 

Is there a approved way to configure or otherwise use galaxy to process multiple files with a tool or workflow?  Using FASTQ Groomer on dozens of files individually is excruciating.

Thanks

 

Mark




This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/
Jennifer Hillman-Jackson
http://galaxyproject.org