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Question: Join And Sort In Galaxy
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gravatar for Felix Hammer
7.8 years ago by
Felix Hammer • 200
Felix Hammer • 200 wrote:
Hello, I have some questions about the Join and Sort tools in Galaxy. How are they implemented? Just the standard unix sort and join? I have a quite large tab file (~1,5 million lines), I want to join with a somewhat smaller file (~20 000 lines). How long will this approximately take? Is there a way to view the progress? Can I gain performance if do a sort on the column I want to join? thx, Felix
galaxy • 751 views
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modified 7.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.8 years ago by Felix Hammer • 200
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gravatar for Jennifer Hillman Jackson
7.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Felix, You are correct, the Sort & Join functions are unix based. Even so, sorting before joining is not required and will not make the Join tool run faster. Actual performance will depend on the size the data and the current server load. If a tool job (any) is taking what seems to be a very long time, please try a re-run. If it is still a problem, feel free to send a shared linked to your history and we can take a look to make certain nothing server-side is going on. A method to allow direct user tracking of progress is something the team has been discussing for some time. It is great idea and is on our priority list. Thanks for using Galaxy! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD COMMENT • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k
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