Merge pull request #89 from Arcadia-Science/kcc/sync

[Sync] Pin arcadia-pycolor and update README

README.md

@@ -19,6 +19,8 @@ Because this tool is based on global structural comparisons, note that the resul
 
 ---
 ## Quickstart
+The ProteinCartography pipeline supports Linux and macOS operating systems; it does not work on Windows. It also requires that you have `conda` or `mamba` installed. If you have an M series Mac, you will need to install an x86-64 version of `conda`. See [below](#running-the-pipeline-on-an-m-series-mac) for some tips on how to do this.
+
 1. Clone the GitHub repository.
     ```
     git clone https://github.com/Arcadia-Science/ProteinCartography.git
@@ -45,9 +47,20 @@ Because this tool is based on global structural comparisons, note that the resul
 
 ---
 ## Compute Specifications
-We have been able to successfully run the pipeline on macOS and Amazon Linux 2 machines with at least 8GB RAM and 8 cores.\
+We have been able to successfully run the pipeline on macOS and Amazon Linux 2 machines with at least 8GB RAM and 8 cores.
+
 For the data generated for our pub, we ran the pipeline on an AWS EC2 instance of type `t2.2xlarge` (32 GiB RAM + 8 vCPU).
 
+## Running the pipeline on an M-series Mac
+To run the pipeline on an M-series Mac (with arm64 architecture), you will need to install an x86-64 version of `conda`. One way to do this is to install Miniconda using the x86-64 `.pkg` installer from the [miniconda website](https://docs.anaconda.com/free/miniconda/). Your Mac should recognize that the installer is for x86-64 and automatically use Rosetta 2 to run it. Alternatively, you can run the `conda` installer script from the command line with the `arch -x86_64` command. For example:
+
+```bash
+curl -O  https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+arch -x86_64 /usr/bin/env bash Miniconda3-latest-MacOSX-x86_64.sh
+```
+
+The x86 version of `conda` will automatically install x86-64 versions of all packages. If you have already installed `conda` on your M-series Mac, be careful to install the x86 version in a different location. To check that you are using the correct version of `conda`, you can run `conda info` and look for the `platform` field in the output. It should say `osx-64`. 
+
 ---
 ## Modes
 The pipeline supports two modes: **Search** and **Cluster**. Both modes are implemented in the same [`Snakefile`](Snakefile). The mode in which the pipeline runs is controlled by the `mode` parameter in the [`config.yml`](config.yml) file.

envs/cartography_dev.yml

@@ -34,4 +34,4 @@ dependencies:
   - wordcloud=1.9.2
 
   - pip:
-      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git#egg=arcadia_pycolor"
+      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git@245ad0c#egg=arcadia_pycolor"

envs/cartography_tidy.yml

@@ -12,5 +12,5 @@ dependencies:
   - mamba=1.4.2
   - pip=23.2.1
   - pip:
-      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git#egg=arcadia_pycolor"
+      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git@245ad0c#egg=arcadia_pycolor"
       - bioservices==1.11.2

envs/plotting.yml

@@ -14,4 +14,4 @@ dependencies:
   - scipy=1.11.4
   - pip=23.2.1
   - pip:
-      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git#egg=arcadia_pycolor"
+      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git@245ad0c#egg=arcadia_pycolor"