How to integrate Trim Galore in Galaxy?

sachitad · 10-03-2012, 02:27 AM

Hello. I have downloaded and installed Trim Galore in my local machine. Now I want to integrate it into Galaxy. I know the procedure to add tool into Galaxy and I have added quite a few: Bismark, FastQ etc. Those Bismark, FastQ was made available by someone with .xml files. I want to know, if someone else has added Trim Galore in Galaxy. If someone knows, please provide me the link. Thanks.

fubar · 10-03-2012, 06:05 AM

Quote:

Originally Posted by sachitad

. I want to know, if someone else has added Trim Galore in Galaxy.

Hi Sachitad,
If you can't find a wrapper in the main Galaxy toolshed, then maybe ask on the Galaxy user list - please see some suggestions for getting a good result at http://wiki.g2.bx.psu.edu/Support#Pu..._A_discussions

fkrueger · 10-19-2012, 03:54 AM

As far as I am aware a Galaxy wrapper for Trim Galore is currently under review (contributed by B. Gruening, Freiburg). We have just released a new version of Trim Galore that adds a couple of features that became necessary/usful for its integration into Galaxy:

- Added option '-o/--output_directory' to redirect all output (including temporary files) to another folder (required for implementation into Galaxy)
- Added option '--no_report_file' to suppress a report file
- Added option '--suppress_warn' to suppress any output to STDOUT or STDERR

Trim Galore can be found here.

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10-03-2012, 02:27 AM	#1
sachitad Junior Member Location: Kathmandu, Nepal Join Date: Oct 2012 Posts: 4	How to integrate Trim Galore in Galaxy? Hello. I have downloaded and installed Trim Galore in my local machine. Now I want to integrate it into Galaxy. I know the procedure to add tool into Galaxy and I have added quite a few: Bismark, FastQ etc. Those Bismark, FastQ was made available by someone with .xml files. I want to know, if someone else has added Trim Galore in Galaxy. If someone knows, please provide me the link. Thanks.

10-19-2012, 03:54 AM	#3
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 625	As far as I am aware a Galaxy wrapper for Trim Galore is currently under review (contributed by B. Gruening, Freiburg). We have just released a new version of Trim Galore that adds a couple of features that became necessary/usful for its integration into Galaxy: - Added option '-o/--output_directory' to redirect all output (including temporary files) to another folder (required for implementation into Galaxy) - Added option '--no_report_file' to suppress a report file - Added option '--suppress_warn' to suppress any output to STDOUT or STDERR Trim Galore can be found here.