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Published 20 hours ago • verified publisher icon bgruening

Visualization (trackster) do not working?

Open vebaev opened this issue 7 years ago • 5 comments

I have tried to visualize GFF, BAM and other file on a genome but on every file format I got error with red track saying "could not loaded due to error". Along that error in the trackster browserI got in the history jobs duplicate job in red with error like the screenshots: https://s27.postimg.org/4r72zptgz/Screen_Shot_2017_01_17_at_14_17_10.png https://s24.postimg.org/kncs12phh/Screen_Shot_2017_01_17_at_14_38_52.png

And so far I couldn't get trackster to work?

PS I have associated the genome database before that properly on each file.

vebaev avatar Jan 17 '17 12:01 vebaev

Further details; When I add a sorted BAM to visualization i got:

/export/galaxy-central/database/job_working_directory/000/750/tool_script.sh: line 9: bedtools: command not found
/export/galaxy-central/database/job_working_directory/000/750/tool_script.sh: line 9: bedGraphToBigWig: command not found

vebaev avatar Feb 22 '17 21:02 vebaev

You mean Trackster?

bgruening avatar Feb 22 '17 21:02 bgruening

Yes

vebaev avatar Feb 22 '17 21:02 vebaev

Hi Vebaev,

I am getting similar error as yours on using galaxy Trackster. Could you resolve the error?

mahesnidhi avatar Apr 05 '17 05:04 mahesnidhi

I am getting the same error. Galaxy can't seem to locate the ucsc tools for converting file formats when producing trackster tracks. Where should these be installed?

swebb1 avatar Feb 19 '20 13:02 swebb1