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-   -   How to integrate Trim Galore in Galaxy? (http://seqanswers.com/forums/showthread.php?t=23812)

sachitad 10-03-2012 02:27 AM

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.

fubar 10-03-2012 06:05 AM

Quote:

Originally Posted by sachitad (Post 85537)
. 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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