Closed manoaman closed 4 years ago
I think I figured out manual setup with Python 3.7.8 instead of Python 3.8.5.
Hi manoaman,
You'll need to attach some credentials to Igneous in order for it to work right. If you're not using Google Cloud Storage, that's a bug, but if you are, you can try providing your cloudvolume credentials to the docker like so:
docker run --env SQS_URL=URL_TO_SQS_QUEUE -v $HOME/.cloudvolume/secrets:/root/.cloudvolume/secrets seunglab/igneous
Running from the repository:
$ python igneous/task_execution.py --queue QUEUE_URL
Can you show me the kimimaro error?
Hi William,
For python 3.8.5, I'm not seeing the same errors from a couple days ago but it still seems to complain for missing module when I run igneous.
% python igneous.py
Traceback (most recent call last):
File "igneous.py", line 5, in <module>
import igneous.task_creation as tc
File "/MyDir/igneous/igneous/__init__.py", line 3, in <module>
from .tasks import *
File "/MyDir/igneous/igneous/tasks/__init__.py", line 1, in <module>
from .skeletonization import SkeletonTask, UnshardedSkeletonMergeTask, ShardedSkeletonMergeTask
File "/MyDir/igneous/igneous/tasks/skeletonization.py", line 23, in <module>
import kimimaro
File "/Users/username/opt/anaconda3/lib/python3.8/site-packages/kimimaro/__init__.py", line 18, in <module>
from .intake import skeletonize, DimensionError, synapses_to_targets
File "/Users/username/opt/anaconda3/lib/python3.8/site-packages/kimimaro/intake.py", line 41, in <module>
import kimimaro.trace
File "/Users/username/opt/anaconda3/lib/python3.8/site-packages/kimimaro/trace.py", line 26, in <module>
import dijkstra3d
ModuleNotFoundError: No module named 'dijkstra3d'
As for the Docker solution, no, I am not using Google Cloud Storage. Could I run Docker without using GCS?
Thanks, m
I'll give a more complete answer when I'm back at my computer but this could be due to a corrupted environment. Have you tried reinstalling from a clean environment?
On Fri, Sep 4, 2020, 4:57 PM manoaman notifications@github.com wrote:
Hi William,
For python 3.8.5, I'm not seeing the same errors from a couple days ago but it still seems to complain for missing module when I run igneous.
% python igneous.py Traceback (most recent call last): File "igneous.py", line 5, in
import igneous.task_creation as tc File "/MyDir/igneous/igneous/init.py", line 3, in from .tasks import * File "/MyDir/igneous/igneous/tasks/init.py", line 1, in from .skeletonization import SkeletonTask, UnshardedSkeletonMergeTask, ShardedSkeletonMergeTask File "/MyDir/igneous/igneous/tasks/skeletonization.py", line 23, in import kimimaro File "/Users/username/opt/anaconda3/lib/python3.8/site-packages/kimimaro/init.py", line 18, in from .intake import skeletonize, DimensionError, synapses_to_targets File "/Users/username/opt/anaconda3/lib/python3.8/site-packages/kimimaro/intake.py", line 41, in import kimimaro.trace File "/Users/username/opt/anaconda3/lib/python3.8/site-packages/kimimaro/trace.py", line 26, in import dijkstra3d ModuleNotFoundError: No module named 'dijkstra3d' As for the Docker solution, no, I am not using Google Cloud Storage. Could I run Docker without using GCS?
Thanks, m
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Yes, you can run Docker without using GCS, you might need AWS SQS though.
Yes, I think I've tried reinstalling from clean environment. It fails with 3.8.5.
It looks like I messed up packaging the MacOS 3.8 version of dijkstra3d somehow. I'm repairing the package.
Okay! dijkstra3d 1.5.1 is released. Try pip install dijkstra3d --upgrade
and let me know if that fixes things for you.
Working great now. Thank you William!
Hi,
I'm trying to set up igneous on macOS Catalina and having issues with both pre-build Docker and manual installation. Do you suggest any workaround for setting up igneous on Catalina?
and kimimaro seems to fail during build when running
pip install -r requirements.txt
.Thank you, manoaman