Having sent this note about three weeks ago and had no response, maybe the question I should have asked would be this :


Has anyone ever successfully used fastx barcode-splitter.pl  inside galaxy ?



If so how did you then get the resulting split files back into the galaxy workflow stream?

alternatively how do I ask the galaxy admins the same question?

Thanks

Jan Szubert

---------- Forwarded message ----------
From: Marek Szubert <marek.szubert@gmail.com>
Date: 8 December 2010 10:49
Subject: fastx barcode-splitter
To: galaxy-user@lists.bx.psu.edu


Hi

I have been looking into galaxy with a view to finding a platform target for developing code.  It is a very ambitious project, and you deserve congratulations for all the development work that has gone into it so far.

I have just started using the fastx barcode splitter tool and found that the job successfully completed with a tabular list of links to display results files contents. When I  run a 'get data - upload file from your computer' to load these split files into the galaxy system (as they do not seem to appear in the history list nor are they automatically accessible to Galaxy for some strange reason), I can only do this using the URL input field  (of  get data - upload file from your computer'), then the task fails and get error :

http://localhost:8080/datasets/2d9035b3fc152403/display/Clip_on_data_12__429.txt
An error occurred running this job: The uploaded file contains inappropriate HTML content

The fastx documentation say the split files should be written to  /tmp , but that it not accessible on the public server  the files are not there on my installation.

Could anyone suggest alternative working methods for reloading the barcode split files?

thanks

Dr Jan Szubert