HI, not sure how to start a new query so will add this one. I am trying to create a Krona chart but all I can see in snapshot is an empty circle. The input file looks fine. Several columns with heirarchical taxonomy. Any ideas ? This is the html file https://help.galaxyproject.org/t/basic-edna-…

Hi @Adam_Hillier On the homepage, under Citing Galaxy, you can read our latest publication for more details: https://galaxyproject.org/citing-galaxy/ << see for more publications https://academic.oup.com/nar/article/52/W1/W83/7676834 << 2024 Update To get a better idea of scientific/region…

This is the Krona html file if it helps [image] Basic eDNA worklow Hi, would like to use Galaxy to build an eDNA workflow pipeline to process Metabarcoding data from Illumina. Is this possible or are there other open source tools available to do this ? Basic…

Hi @Adam_Hillier Glad to learn you have made some progress! I moved this over into a new topic so we can focus on the new tool error. If you want to share your history with the work, we can try to help resolve the error. How to generate a history share link is explained here → FAQ: Sharing your Hi…

HI Jenna, Thanks for picking this up. I have looked in to inside and outside Galaxy and haven[t had much luck. I have also looked on online forums. It seems to be a known issue but I can’t fond the answer. It looks like Krona plots should should be very easy. I will get back to you with the histo…

Hi Jenna, One more question. Are Nextflow your main ‘rivals’ so to speak ? https://mail.google.com/mail/u/0/#inbox/WhctKLbmpGrcvTVNCtLfndwKbTTRHfvszHqxTQthpCnLrwsvHTfCdslclkJRdfCVmxPbdcL Adam

HI Jenna, Attached is an example of the kind of work I do. I just found the comparison matrix below which is quite helpful. As I am self taught I want something easy to use (not programming language level if possible) and Galaxy seems to tick that box perhaps more than any other. My workflows wi…

We can help to troubleshoot here. Issues are usually with how the data is formatted versus what was expected. That same job (inputs, parameters, tool) would fail anywhere, not just in Galaxy, since the hosted tool is still just the original underlying tool run on a computing cluster somewhere. …

HI Jenna, This is my work flow. which is very simple, [D3168359-0CCC-4B33-BB0B-99FD396D9FBD.jpeg] This is my input data table which looks fine [E8BB11D6-6933-4CA8-A739-74891E13C97F.jpeg] This is what I get from Krona Plot [63DB1C17-6D89-4B04-8A43-384A293DB692.jpeg] This is what i see when …

Yes, I agree the problem here is probably ‘underneath’ Galaxy. I get the same problem when I run Krona plot from a bash terminal. Adam

Thanks for sharing the screenshots @Adam_Hillier ! Very helpful and I see the problem. Krona is looking for a count value in the first column, then categories in the others. Your file is missing that first value. This is the Help from the tool form (scroll down to find this, plus links to the origi…

HI Jenna, To be honest I did not find https://galaxyproject.org very useful at all to answer my questions. Thee should be a font page explaining what Galaxy is about. Is it about bioinformatics ? It says it can be used for analysing data. Bioinformatics data only ? Anything else ? What about astr…

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Krona troubleshooting

troubleshooting, taxonomy_krona_chart

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