Finally, if you would like to install the necessary requirements locally, we suggest using Mamba:
- If you do not have any pre-existing conda installation, install Mamba and use mambaforge.
- In case you have a pre-existing conda installation, you can install Mamba by either:
- Using the recommended way to install Mamba from mambaforge. This will not invalidate your conda installation, but possibly your pre-existing conda envs will be in a different location (e.g.
/Users/USER_NAME/opt/anaconda3/envs/
) then the new mamba envs (e.g./Users/USER_NAME/mambaforge/envs/
). You can verify this by runningconda env list
. The addition ofexport CONDA_ENVS_PATH=/Users/user/opt/anaconda3/envs/
into your.bashprofile
or.zprofile
file will fix this. - Use the Existing conda install way, i.e. run
conda install mamba -n base -c conda-forge
whilst in the base environment. This way can take much longer time than the recommended way described above, and might not lead to a successful installation, especially if run on arm64 (Apple Silicon) OS X.
- Using the recommended way to install Mamba from mambaforge. This will not invalidate your conda installation, but possibly your pre-existing conda envs will be in a different location (e.g.
To avoid conflict with used packages, we have prepared several environments:
Day_5/environment_basic.yml
, Day_5/environment_cellpose.yml
, Day_5/environment_conversion.yml
, Day_5/environment_minio.yml
and Day_5/environment_cp.yml
.
Create the environments. For this, first run the commands below as written, then replace Day_5/environment_conversion.yml
motives with Day_5/environment_cellpose.yml
, Day_5/environment_basic.yml
, Day_5/environment_cp.yml
or Day_5/environment_minio.yml
and run again to create the other envs.
For Windows, OS X x86_64 (NOT arm64 Apple Silicon), Linux:
$ git clone https://github.com/ome/EMBL-EBI-imaging-course-04-2024
$ cd EMBL-EBI-imaging-course-04-2024
$ mamba env create -f Day_5/environment_conversion.yml
For OS X arm64 Apple Silicon
$ git clone https://github.com/ome/EMBL-EBI-imaging-course-04-2024
$ cd EMBL-EBI-imaging-course-04-2024
$ CONDA_SUBDIR=osx-64 mamba env create -f Day_5/environment_conversion.yml
and activate the newly created environment:
$ conda activate imaging_course_conversion_day5_2024
Before creating a new environment, remember to deactivate the current one:
$ conda deactivate
See also Conda command reference.
The following steps are only required if you want to run the notebooks.
- If you have Anaconda installed:
- Start Jupyter from the Anaconda-navigator
- In the conda environment, run
mamba install ipykernel
(for OS X Apple SiliconCONDA_SUBDIR=osx-64 mamba install ipykernel
) - To register the environment, run
python -m ipykernel install --user --name imaging_course_conversion_day5_2024
- Select the notebook you wish to run and select the
Kernel>Change kernel>Python [conda env:imaging_course_conversion_day5_2024]
orKernel>Change kernel>imaging_course_conversion_day5_2024
- If Anaconda is not installed:
- Add the virtualenv as a jupyter kernel i.e.
ipython kernel install --name "imaging_course_conversion_day5_2024" --user
- Open jupyter notebook i.e.
jupyter notebook
and select theimaging_course_conversion_day5_2024
kernel or[conda env:imaging_course_conversion_day5_2024]
according to what is available.
- Add the virtualenv as a jupyter kernel i.e.
To stop the notebook server, in the terminal where te server is running, press Ctrl C
. The following question will be asked in the terminal Shutdown this notebook server (y/[n])?
. Enter the desired choice.