Conda activate in script

Question

To run a Python program I take run the following manually:

conda activate sentence-splitter-service
python3 scripts/serve.py  /opt/acorn/file-stream/acorn-sentence-request-local /opt/acorn/file-stream/acorn-language-request-local /opt/acorn/file-stream/acorn-document-response-local  --port 8887

Can I run both of these in a shell script?

You should be able to run pretty much anything in a shell script. Have you tried it? What problems did you encounter? — Sarah Messer
– Sarah Messer, Commented Dec 28, 2021 at 20:34
Yes, you can. Whether it does what you want it to do is a separate question entirely, but since you haven't told us what the desired behavior is nor given us the contents of your scripts, we can't answer that question for you. — BrokenBenchmark
– BrokenBenchmark, Commented Dec 28, 2021 at 20:35

C.Nivs · Accepted Answer · 2021-12-28 20:42:23Z

5

conda activate is for an interactive shell only (i.e. not a shell script). If you want a specific env to run a script, then use conda run -n sentence-splitter-service python scripts/serve.py ... where -n specifies the environment name. As an example:

# This shows that my virtualenv is indeed on my path
conda run -n testenv python -c 'import sys; print(sys.path)'
['', 'C:\\Users\\cn18933\\Miniconda3\\envs\\testenv\\python38.zip', ...]

answered Dec 28, 2021 at 20:42

C.Nivs

13.2k3 gold badges21 silver badges48 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

merv · Accepted Answer · 2021-12-29 18:47:41Z

2

I believe using conda run should be the preferred solution, however, one can also use the shebang to indicate the shell should run in login-mode:

script.sh

#!/usr/bin/env bash -l
conda activate sentence-splitter-service
python3 scripts/serve.py  /opt/acorn/file-stream/acorn-sentence-request-local /opt/acorn/file-stream/acorn-language-request-local /opt/acorn/file-stream/acorn-document-response-local  --port 8887

This assumes that the user executing the script has run conda init to configure their shell resource file (e.g., .bashrc or .bash_profile) to initialize the Conda shell functionality.

answered Dec 29, 2021 at 18:47

merv

78.1k17 gold badges217 silver badges286 bronze badges

2 Comments

Woodsman Over a year ago

I tried the shebang as you have in line 1 above, but got "/usr/bin/env: bash -l: No such file or directory

merv Over a year ago

@Woodsman Can depend on your system. Another variant is simply #!/bin/bash -l (i.e., don't assume bash is currently on PATH). For Windows, I'm not sure what the alternative is.

Collectives™ on Stack Overflow

Conda activate in script

2 Answers 2

Comments

2 Comments

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

2 Comments

Related