- (at commandline) git clone https://github.com/pnnl/AutoMicroED.git
- (This git clone is required only once. This does not need to be repeated everytime a user needs to run AutoMicroED.)
- Install (once)
- For more efficient library management (do not complicate other environments), we recommend
- install conda from https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
- conda activate (conda name)
- then, install below.
- However, it is fine to install without conda environment management.
- pip install -r /requirements.txt
- compile generate_adx (optional)
- copy generate_adx_source_file to user's folder
- gfortran -O -C generate_adx.f90 -o generate_adx
- Estimated install time: 5 minutes with fresh conda environment set-up. Less time without conda set-up.
- For more efficient library management (do not complicate other environments), we recommend
- Refer
- (Some software may not be installed in WindowsOS.)
- Designate PATH for tvips, XDS and ccp4
- For example, for bash user
- add
- export PATH="/Users/kimd999/research/microED/dn_try/tvips-tools-jiffies-20191209-macos64/":$PATH
- export PATH="/Users/kimd999/bin/XDS-OSX_64/":$PATH
- export PATH="/Applications/ccp4-7.0/bin/":$PATH
- into ~/.bashrc
- add
- For example, for bash user
- Alternatively, AutoMicroED user can specify locations of binary at args_file. Refer templates/input_files for examples and explanations.
- If user's OS doesn't have git
- If a user sees the error message during git clone, “Permission denied (publickey).fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists.”,
- User’s computer needs to be registered to his/her github account.
- Therefore, make/log in github account (free).
- Generate a new SSH key
- Add a new SSH key to your GitHub account
- If user's macOS shows, “xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.”
- Download commandline as instructed (this may take ~7 minutes)