Daemon Issue

[sadler7]

Everything has been downloaded successfully except for Docker, which still gives me the same daemon error. I've rerun the installation multiple times and rebooted, with little avail.

root@DESKTOP-H31OUEN:~/GALES/bin# ./run_prok_pipeline -i ../test_data/genomes/E_coli_k12_dh10b.fna -od /tmp/demo -v cheetah -rd /dbs
Starting pipeline. If this is your first time running this pipeline there will be some latency as the necessary Docker images are downloaded. This is a one-time cost.
Running command: cwl-runner --outdir /tmp/demo /tmp/demo/prok-annotation-cheetah.cwl /tmp/demo/prok-annotation-cheetah.json
/usr/local/lib/python2.7/dist-packages/cwltool/init.py:17: CWLToolDeprecationWarning:
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

""", category=CWLToolDeprecationWarning)
INFO /usr/local/bin/cwl-runner 1.0.20191225192155
INFO Resolved '/tmp/demo/prok-annotation-cheetah.cwl' to 'file:///tmp/demo/prok-annotation-cheetah.cwl'
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?
ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: cwltool requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim
ERROR: Return code 1 when running the following command: cwl-runner --outdir /tmp/demo /tmp/demo/prok-annotation-cheetah.cwl /tmp/demo/prok-annotation-cheetah.json
root@DESKTOP-H31OUEN:~/GALES/bin# ./view_annotation -i /tmp/demo -f ../test_data/genomes/E_coli_k12_dh10b.fna
Traceback (most recent call last):
File "./view_annotation", line 18, in
from biocode import utils, gff
ModuleNotFoundError: No module named 'biocode'

Thanks in advance.

-Sean

[jorvis]

You need to be sure you can do the steps for testing a docker installation before trying to run GALES. Here's a place to start:

https://docs.docker.com/get-started/

[sadler7]

I'm updating Windows as I type this. I went straight to Ubuntu and appreciate your patience. Thanks for the help.

[sadler7]

Thanks again for helping with Docker. Here's the igraph error I'm getting with the biocode/jinja2 download:

----------------------------------------

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-nk4kddsg/python-igraph/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-1r8dq_2o-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-nk4kddsg/python-igraph/

[jorvis]

Can you give a little more info? What command did you run to get that error, which Ubuntu version are you using, and can you post a more complete output (even if it's a file attachment).

[sadler7]

I created a log file filled with the output from "sudo pip3 install biocode jinja2", but was denied the rights to push it so I'll email it. Here's a copy of the error scripts:

Failed building wheel for python-igraph

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-o7futrik/python-igraph/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-zbvdamco-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-o7futrik/python-igraph/

[sadler7]

Here's a copy of the output, not sure if the error scripts were also loaded into the file. Version: Ubuntu 18.04 LTS Best, Sean

…

________________________________ From: Joshua Orvis <[email protected]> Sent: Tuesday, August 11, 2020 9:12 AM To: jorvis/GALES <[email protected]> Cc: Sean Adler <[email protected]>; Author <[email protected]> Subject: Re: [jorvis/GALES] Daemon Issue (#27) External Email - Use Caution Can you give a little more info? What command did you run to get that error, which Ubuntu version are you using, and can you post a more complete output (even if it's a file attachment). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjorvis%2FGALES%2Fissues%2F27%23issuecomment-672005907&data=02%7C01%7Csadler7%40jhu.edu%7C614bfb9b36be4311938808d83e08f615%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637327555512872407&sdata=ESK1kB2Lzbmw48wM%2Bou1GGDUYgXRH84OA5s1VI7H8XU%3D&reserved=0>, or unsubscribe<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAP6KWZ67XPBIHMLMHGYCQITSAFNVVANCNFSM4PYMDEAQ&data=02%7C01%7Csadler7%40jhu.edu%7C614bfb9b36be4311938808d83e08f615%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637327555512882403&sdata=7hUbbc5wU72gQuySXUKR4g77YfNzCQ10LQotiXOq5cM%3D&reserved=0>.

[sadler7]

Is there a chance you can repost the URL you PM'd me in office hours before I try a binary installation? I can run the docker command without the daemon issue now, but still get the same E:/ drive error when I run the installation you posted on the GALES Github and get error messages about the Daemon whenever I test it with "sudo docker run hello world". I've uninstalled and rebooted numerous times, tried manually rewriting the .json, and enabling seccomp. I downloaded igraph via brew w/o issues.