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Installation

Prerequisites

ASAP requires Render web service (https://github.com/saalfeldlab/render) to be installed for storing and processing the data. Please refer to Render for details on its installation.

Installing ASAP-modules

ASAP can be installed using the following commands.

Clone this repository

# git clone this repository
git clone https://github.com/AllenInstitute/asap-modules .

Install from source

CD to the cloned directory and run setup.py

python setup.py install

Docker setup

You can also install asap-modules using the provided docker file

docker build -t asap-modules:latest --target asap-modules .

Running docker

The built docker image can then be run using the following command

docker run --rm asap-modules:latest

Running modules of ASAP

Once ASAP is installed using the above command, you can use all of its functionalities as follows;

python -m asap.<submodule>.<function_to_run> --input_json <input_json_file.json> --output_json <output_json_file.json>

For example, the montage qc module can be run using the following command.

python -m asap.em_montage_qc.detect_montage_defects --input_json <your_input_json_file_with_required_parameters> --output_json <output_json_file_with_full_path>

and here is an example input json file for the detect_montage_defects module

{
    "render":{
        "host": <render_host>,
        "port": <render_port>,
        "owner": <render_project_owner>,
        "project": <render_project_name>,
        "client_scripts": <path_to_render_client_scripts>
    },
    "prestitched_stack": <pre_montage_stack>,
    "poststitched_stack": <montaged_stack>,
    "match_collection_owner": <owner_of_point_match_collection>,
    "match_collection": <name_of_point_match_collection>,
    "out_html_dir": <path_to_directory_to_store_the_qc_plot_html_file>,
    "plot_sections": <True/False>,
    "minZ": <z_index_of_the_first_section_to_run_qc_for>,
    "maxZ": <z_index_of_the_last_section_to_run_qc_for>,
    "neighbors_distance": <qc_parameter>,
    "min_cluster_size": <qc_parameter>,
    "residual_threshold": <qc_parameter>,
    "pool_size": <pool_size_for_parallel_processing>
}

The list of parameters required for each module can be found out using the –help option.

# find the list of parameters for the solver module using its help option
python -m asap.solver.solve --help