Hello, just wanted to say thank you for the plugin.
I've used it only recently, but it has quickly become my favorite for taxonomy visualization.
Thanks a lot!
Valentyn
4 Likes
Hello, Thank you so much for the plugin !
1 Like
4 off-topic replies have been split into a new topic: access community plugins through artifact API?
Please keep replies on-topic in the future.
Hi, in Qiime2 2023.2 I get the message
"Plugin error from krona: 'ktImportText' is not found, but can be installed with:
conda install -c bioconda krona
Debug info has been saved to /tmp/qiime2-q2cli-err-uvk1rq1z.log"
However, if I install as said do
$ conda install -c bioconda krona
"Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: | Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort."
etc. with a lot of package conflicts.
Has anything changed in the newer Qiime that makes this happen? In 2021.11 version it worked, but I upgraded to 2023.2 a few weeks ago.
1 Like
Hello Jack,
I had no problems installing krona via conda and q2-krona via pip, but conda sometimes have problems solving environments.
I'm no expert on this but I can suggest two things.
First, you can try to update conda, and try to install krona again.
Second, you might want to try mamba. Mamba helped me solve such problems before, and as a plus, mamba is definitely faster than conda.
Keep us updated on this please,
Good luck,
Kaan
Edit: I did not mention q2 version. Yes, I installed them in 2023.2 version.
3 Likes
@the_dummy your plugin in publication! https://www.researchgate.net/publication/368474706_A_first_insight_into_the_Polish_Bochnia_Salt_Mine_metagenome
1 Like
Hi the_dummy, I used to run Qiime2 under Ubuntu 22.04 LTS on a separate computer, but I needed to temporarily switch to Windows 10 WSL (version 2, running an Ubuntu 20.04 version). Here I could download and install Krona in version 2023.2 without any error messages.
Conda was updated to its latest version, but again I get:
Plugin error from krona:
'ktImportText' is not found, but can be installed with:
conda install -c bioconda krona
Which was already installed successfully.
Note: 'ktImportText' is present in ~/miniconda3/bin
When I have time I will try mamba and let you know the result.
Hello @jack2017,
I have zero experience on and knowledge about Windows 10 WSL. But the main thing is 'ktImportText' can not be found on PATH.
This could be a problem due to conda not changing PATH information even if you activate the environment.
If this was an issue on an Ubuntu machine, I would recommend to check if something is wrong with .bashrc file, so there could be something similar.
Best wishes,
Kaan
2 Likes