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conda config #12

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conda config #12

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74d9fdb
update gitignore, add environment yml
wadeschulz Mar 13, 2024
d03a3b9
update readme to switch to miniconda
wadeschulz Mar 13, 2024
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5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -190,4 +190,7 @@ testingenv/
HPAv18RBGY_wodpl.csv
HPAv18/
download_images.py
settings.json
settings.json

data/
results/
17 changes: 15 additions & 2 deletions README.adoc
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Expand Up @@ -21,16 +21,29 @@ up an issue here on Github or by contacting @cwinsnes.

== Installation and Setup
NOTE: It is recommended to run the module in a separate virtual environment
such as https://www.anaconda.com/[Anaconda] or
such as https://conda.io/projects/conda/en/latest/user-guide/install/linux.html[miniconda] or
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I believe this should link to the Miniconda page rather than the linux install.

https://docs.anaconda.com/free/miniconda/

https://docs.python.org/3/library/venv.html[venvs]
to avoid any issues with package versions.

Installing the required modules for this package can be done through `pip`.
If using miniconda, the environment can be installed by running:
[,bash]
----
python env create -f environment.yml
----

After your environment is created, activate it with:
[,bash]
----
conda activate cm4ai-hpa
----

Or after creating a separate environment, the required modules can be installed with `pip`.
[,bash]
----
python -m pip install -r requirements.txt
----


=== Data
The model requires the input images to be stored in the following way:

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11 changes: 11 additions & 0 deletions environment.yml
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@@ -0,0 +1,11 @@
name: cm4ai-hpa
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Not entirely sure on this default name. What does cm4ai mean?

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CM4AI is Cell Maps for AI - the name of our DGP within Bridge2AI

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@cwinsnes Sorry that we forgot to inform you! The CM4AI project is a new large collaborative project that the lundberg lab runs with several other collaborators across the U.S. (e.g., also the Ideker lab). The purpose is to build more and better MuSIC maps. We used the HPA densenet in a hackathon that was part of the CM4AI project and @wadeschulz has been incorporating the densenet into an Azure platform for the hackathon. To do that he had to do a few changes and then I encouraged Wade to send these also as a pull request since I thought these could be helpful for other users in the future. Thank you that you replied @cwinsnes and discuss it!


channels:
- defaults

dependencies:
- python=3.10
- pip

- pip:
- -r requirements.txt