Interactive Jupyter lab enviroment taking a long time to solve an enviroment or failing.

usegalaxy.eu support
1

Hi,

I am trying to run the Generating a single cell matrix using Alevin and combining datasets (bash + R)
Hands-on: Generating a single cell matrix using Alevin and combining datasets (bash + R) / Generating a single cell matrix using Alevin and combining datasets (bash + R) / Single Cell.

I am having trouble getting the environment to solve using the conda environment. For the following lines of code in the terminal environment:

conda install -y -c bioconda bioconductor-tximeta # install this first

conda install -y -c bioconda atlas-gene-annotation-manipulation

conda install -y -c bioconda bioconductor-dropletutils

At first, I couldn’t get any of these lines of code to work or solve but using the following lines of code I got the first two lines to solve.

conda config --add channels r

conda config --set channel_priority flexible

However, the third line of code has been solving for 6 hours plus now and hasn’t finished.

I have previously got the is tutorial to work.

Any help would be brilliant on why this is not solved or taking so long to solve. Happy to provide further info if necessary.

best

Mark

2

Welcome, @Mark_Hintze

The UseGalaxy.eu server was likely just busy. Is everything loaded now?

3

Hi @jennaj,

Thanks for the reply. I don’t think so, when I try the code now I got the following output.
Looking for: [‘atlas-gene-annotation-manipulation’]

bioconda/linux-64 Using cache
bioconda/noarch Using cache
r/linux-64 Using cache
r/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/main/noarch [====================] (00m:00s) No change
pkgs/main/linux-64 [====================] (00m:00s) No change
pkgs/r/linux-64 [====================] (00m:00s) No change
pkgs/r/noarch [====================] (00m:00s) No change
Killed

and I can’t install using either Conda or Mamba. (popped in a screenshot - not sure if this will work)

image
image1547×926 29 KB

The tutorial and code worked previously, I am not sure if it is something to do with my setup or if something has changed in the tool?

best and thanks for the help,

mark

4

seems to be all conda installations for me at the moment.

(base) root@pulsar-60229145-j2tb7:/pulsar_staging/60229145/working/jupyter# conda install -c r ggplot
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): - Killed
(base) root@pulsar-60229145-j2tb7:/pulsar_staging/60229145/working/jupyter# conda install -c r dplyr
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): | Killed

best

Mark

5

Hi @Mark_Hintze

Thanks for the followup!

I wasn’t able to get an Interactive JupyterLab Notebook to launch at all at the UseGalaxy.eu server – yesterday or today.

Testing history: https://usegalaxy.eu/u/jenj/h/test-gtn-jupyter-lab-sept-2024

Let’s ping the EU administrators to see if more is going on: @wm75 or maybe @bjoern.gruening can you help?

6

Sorry for the inconvenience. I just wanted to say that this is working now. We just passed the 10.000 Jupyter runs :slight_smile: