Merge pull request #172 from CellProfiler/mccruz07-patch-2

Update Installation_instructions_for_CellProfiler_M1.md

Author: callum-jpg

…tion_instructions_for_CellProfiler_M1.md …ons_M1_CellProfiler_CellPose_Stardist.mdInstructions/Installation_instructions_for_CellProfiler_M1.md renamed to Instructions/Installation_instructions_M1_CellProfiler_CellPose_Stardist.md Instructions/Installation_instructions_for_CellProfiler_M1.md renamed to Instructions/Installation_instructions_M1_CellProfiler_CellPose_Stardist.md

@@ -1,4 +1,4 @@
- Installation instructions for CellProfiler + plugins using a conda environment on Macs using the new Apple M1/2 processor. 
+Installation instructions for CellProfiler, CellProfiler plugins, CellPose and StarDist in a conda environment on Apple silicon.
 
 1. **Install brew**
     ```
@@ -15,18 +15,18 @@
     brew install java
     ```
 
-4. **For the system Java wrappers to find this JDK, symlink it with**
+4. **For the system Java wrappers to find this JDK and symlink it**
     ```
     sudo ln -sfn /opt/homebrew/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk
     ```
 
-5. **Set version in zshrc**
+5. **Set version in .zshrc**
     ```
     echo export JAVA_HOME=$(/usr/libexec/java_home -v 1.8) >> ~/.zshrc
     source ~/.zshrc
     ```
 
-6. **Brew install the packages req**
+6. **Brew install package requirements**
     ```
     brew install freetype mysql git
     ```
@@ -41,52 +41,86 @@
     brew install hdf5@1.12
     ```
 
-9. Make sure to get the version directory correct for the version installed. Find with `ls /opt/homebrew/Cellar/hdf5/`
+9. **Make sure to get the version directory correct for the version installed. Find with `ls /opt/homebrew/Cellar/hdf5/`**
     ```
     export HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.12.1_1/
     ```
-10. **Create a folder and download cellprofiler, cellprofiler-core, and cellprofiler-plugins**
+10. **Create a folder and download cellprofiler-plugins**
 
     ```
     mkdir cp_plugins
     cd cp_plugins
-    git clone https://github.com/CellProfiler/core
-    git clone https://github.com/CellProfiler/CellProfiler
     git clone https://github.com/CellProfiler/CellProfiler-plugins
     ```
 
-11. **Modify the **setup.py** in the cloned CellProfiler repo.**
-    
-    Comment out cellprofiler-core and wxpython from the **install_requires** section, since we are installing our own versions:
-
-    ```
-    ...
-    "boto3>=1.12.28",
-    # "cellprofiler-core==4.2.1",
-    "centrosome==1.2.0",
-    ...
-    "six",
-    # "wxPython==4.1.0",
-    ```
-
-12. **Download and install miniconda**
+11. **Download and install miniconda**
 
    ```
     wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -O ~/miniconda.sh
    ```
 
 
-16. **Create a conda environment using the cellprofiler_plugins_macM1.yml file**
+12. **Create a conda `.yml` file**
+    In a text editor, paste the following test and save it as `cellprofiler_plugins_macM1.yml`:
+    ```
+    name: cpcellpose
+
+    channels:
+    - conda-forge
+    - anaconda
+    - bioconda
+    - defaults
+    - apple
+
+    dependencies:
+    - python=3.8
+    - pip
+    - h5py
+    - mysqlclient
+    - imagecodecs
+    - python.app
+    - pandas
+    - pip:
+        - cellpose
+        - attrdict
+        - sip==5.5.0
+        - boto3>=1.12.28
+        - cellprofiler-core
+        - centrosome==1.2.1
+        - docutils==0.15.2
+        - h5py~=3.6.0
+        - imageio>=2.5
+        - inflect>=2.1
+        - Jinja2>=2.11.2
+        - joblib>=0.13
+        - mahotas>=1.4
+        - matplotlib==3.1.3
+        - mysqlclient==1.4.6
+        - numpy>=1.20.1
+        - Pillow>=7.1.0
+        - prokaryote==2.4.4
+        - python-bioformats==4.0.6
+        - python-javabridge==4.0.3
+        - pyzmq~=22.3
+        - sentry-sdk==0.18.0
+        - requests>=2.22
+        - scikit-image>=0.17.2
+        - scikit-learn>=0.20
+        - scipy>=1.4.1
+        - six
+        - tifffile<2022.4.22
+        - wxPython==4.2.0
+    ```
+
+
+13. **Create a conda environment using the cellprofiler_plugins_macM1.yml file**
 
     At this stage, your folder/file structure should look like this:
 
     ```
     ├── cp_plugins
-        ├── CellProfiler/
         ├── CellProfiler-plugins
-        ├── core
         └── cellprofiler_plugins_macM1.yml
-
     ```
 
     In the terminal, make sure you are in the `cp_plugins` folder mentioned above.
@@ -95,34 +129,21 @@
     conda env create -n cp_plugins --file cellprofiler_plugins_macM1.yml
     ```
 
-17. **Activate the conda environment**
+14. **Activate the conda environment**
 
     ```
     conda activate cp_plugins
     ```
 
-18. **Install Cellprofiler core and cellprofiler**
+15. **Install Cellprofiler core and cellprofiler**
 
-    In the terminal with your environment activate, navigate to the folder where you download the softwares and enter:
+    In the terminal with your environment activate, navigate to the folder where you download the software and enter:
         
     ``` 
-    pip install ./core
-    pip install ./CellProfiler
-    ```
-
-19. **Resolving dependencies conflits**
-
-    In the terminal with your environment activate, enter:
-    ```
-    pip uninstall -y centrosome python-javabridge
-    pip install --no-cache-dir --no-deps --no-build-isolation python-javabridge centrosome
-    pip uninstall matplotlib -y
-    pip install matplotlib==3.2
-    pip uninstall mahotas -y
-    pip install mahotas
+    pip install cellprofiler --no-deps
     ```
 
-20. **Install other packages for other plugins (just for runStardist)**
+16. **Install other packages for other plugins (just for runStardist)**
 
     In the terminal with your environment activate, enter:
     ```
@@ -131,15 +152,15 @@
     pip install stardist csbdeep --no-deps
     ```
 
-21. **Open CellProfiler**
+17. **Open CellProfiler**
 
     Execute this command from within the downloaded CellProfiler repo (get there with `cd CellProfiler`)
 
     ```
     pythonw -m cellprofiler
     ```
 
-22. **Connect CellProfiler with the plugins folder**
+18. **Connect CellProfiler with the plugins folder**
 
     With your environment active, type pythonw -m cellprofiler in terminal to open CellProfiler if it is not open already.
 
@@ -150,6 +171,18 @@
     *Close CellProfiler and reopen it by typing pythonw -m cellprofiler on the command line
 
 
+### Resolving dependencies conflits
+
+    In the terminal with your environment activate, enter:
+    ```
+    pip uninstall -y centrosome python-javabridge
+    pip install --no-cache-dir --no-deps --no-build-isolation python-javabridge centrosome
+    pip uninstall matplotlib -y
+    pip install matplotlib==3.2
+    pip uninstall mahotas -y
+    pip install mahotas
+    ```
+
 ### Test your installation
 
 Add a module to your pipeline by hitting the **+** button in the pipeline panel (bottom left)