02-config-for-image-analysis.Rmd

# (PART) Images to measurements  {-}
# Configure tools to process images
## Download software

You may need to authenticate your GitHub account to be able to clone these:

```sh
cd ~/efs/${PROJECT_NAME}/workspace/
mkdir software
cd software
git clone git@github.com:broadinstitute/cellpainting_scripts.git
git clone git@github.com:broadinstitute/pe2loaddata.git
git clone git@github.com:broadinstitute/cytominer_scripts.git
cd ..
```

To authenticate your GitHub account, follow instructions to setup SSH keys here https://help.github.com/articles/connecting-to-github-with-ssh/.

You can also clone these repos by following the structure below and inputting your OAuth token as necessary.

```sh
git clone https://username@github.com/broadinstitute/cytominer_scripts.git
```

If these repos have already been cloned, `git pull` to make sure they are up to date.

This is the resulting structure of `software` on EFS (one level below `workspace`):
```
└── software
    ├── cellpainting_scripts
    ├── cytominer_scripts
    └── pe2loaddata
```


## Setup Distributed CellProfiler

```sh
cd ~/efs/${PROJECT_NAME}/workspace/software/Distributed-CellProfiler/

pyenv shell 2.7.12

pip install -r files/requirements.txt

```