Windows Problem With bash start_docker.sh Command
Nicholas-Bartelo opened this issue · 2 comments
Hello!
I am attempting to install this package today to use Pixie on a Windows machine. I have made it through the installation tutorial up to the step "Setting up the repo".
Everything seems to be working well until I execute the line bash start_docker.sh in the command prompt terminal. The outcome is the error message in the image below. I ran wsl sudo apt-get install dos2unix and then retried, but this did not work for me.
Please let me know if there is a solution to this problem. I look forward to your response and thank you in advance!
Hi @Nicholas-Bartelo! Sorry about this issue, like you suspect, it's probably a Windows line-ending error. In the lab, we have actually moved away from using docker because it's been causing a lot of issues. Instead, I would suggest running Pixie outside of docker.
To run Pixie outside of docker, create a conda environment with python version 3.11 (actually, 3.9, 3.10, or 3.11 should be okay): conda create -n ark_env python=3.11. Then install ark-analysis using pip install ark-analysis. Seems like you have already cloned the repo, but if not, clone using git clone https://github.com/angelolab/ark-analysis.git. Then navigate into the ark-analysis folder (cd ark-analysis) and start jupyter using jupyter lab. You should be able to then open the notebook 2_Pixie_Cluster_Pixels.ipynb (this notebook lives in the templates folder in ark-analysis, but I suggest making a copy and moving it somewhere else to avoid confusion - the templates folder will overwrite every time you pull from Github).
All the necessary dependencies should be installed after doing pip install. I use a Windows machine and can use Pixie no problem using this method. Please let me know if this works for you.
The bash script specifies the version number in the docker tag which doesn't match up with "ark-analysis:latest."
Unable to find image 'angelolab/ark-analysis:v0.7.1' locally
docker: Error response from daemon: manifest for angelolab/ark-analysis:v0.7.1 not found: manifest unknown: manifest unknown.
See 'docker run --help'.
May I suggest that if you are having problems with the Docker usage, you take down the instructions to make use of it until the problems are addressed?