Metadata-Version: 2.1
Name: fusor
Version: 0.0.25
Summary: Provide computable object representation and validation for gene fusions
Home-page: https://github.com/cancervariants/fusor
Author: Wagner Lab, Nationwide Childrens Hospital
License: MIT
Description: # FUSOR
        
        FUSOR (**FUS**ion **O**bject **R**epresentation) provides modeling and validation tools for representing gene fusions in a flexible, computable structure.
        
        ### Installation
        
        To install FUSOR:
        ```commandline
        pip install fusor
        ```
        
        For a development install, we recommend using Pipenv. See the
        [pipenv docs](https://pipenv-fork.readthedocs.io/en/latest/#install-pipenv-today)
        for direction on installing pipenv in your compute environment.
        
        Once installed, from the project root dir, just run:
        
        ```commandline
        pipenv shell
        pipenv lock && pipenv sync
        ```
        
        #### MacOS Errors
        If you encounter errors, try the following:
        ```commandline
        export SYSTEM_VERSION_COMPAT=1
        pipenv lock && pipenv sync
        ```
        
        ### Data Downloads
        
        #### SeqRepo
        `FUSOR` relies on [seqrepo](https://github.com/biocommons/biocommons.seqrepo), which you must download yourself.
        
        From the _root_ directory:
        ```
        pip install seqrepo
        sudo mkdir /usr/local/share/seqrepo
        sudo chown $USER /usr/local/share/seqrepo
        seqrepo pull -i 2021-01-29  # Replace with latest version using `seqrepo list-remote-instances` if outdated
        ```
        
        If you get an error similar to the one below:
        ```
        PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2021-01-29._fkuefgd' -> '/usr/local/share/seqrepo/2021-01-29'
        ```
        
        You will want to do the following:\
        (*Might not be ._fkuefgd, so replace with your error message path*)
        ```console
        sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/2021-01-29
        exit
        ```
        
        #### UTA
        FUSOR also uses [**C**ommon **O**perations **O**n **L**ots-of **Seq**uences Tool (*cool-seq-tool*)](https://github.com/GenomicMedLab/cool-seq-tool) which uses [UTA](https://github.com/biocommons/uta) as the underlying PostgreSQL database.
        
        _The following commands will likely need modification appropriate for the installation environment._
        1. Install [PostgreSQL](https://www.postgresql.org/)
        2. Create user and database.
        
            ```
            $ createuser -U postgres uta_admin
            $ createuser -U postgres anonymous
            $ createdb -U postgres -O uta_admin uta
            ```
        
        3. To install locally (location does not matter):
        ```
        export UTA_VERSION=uta_20210129.pgd.gz
        curl -O http://dl.biocommons.org/uta/$UTA_VERSION
        gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5433
        ```
        
        ##### UTA Installation Issues
        If you have trouble installing UTA, you can visit [these two READMEs](https://github.com/ga4gh/vrs-python/tree/main/docs/setup_help).
        
        ##### Connecting to the UTA database
        To connect to the UTA database, you can use the default url (`postgresql://uta_admin@localhost:5433/uta/uta_20210129`). If you use the default url, you must either set the password using environment variable `UTA_PASSWORD` or setting the parameter `db_pwd` in the `FUSOR` class.
        
        If you do not wish to use the default, you must set the environment variable `UTA_DB_URL` which has the format of `driver://user:pass@host:port/database/schema`.
        
        #### Gene Normalizer
        
        `FUSOR` also relies on data from [gene-normalizer's](https://github.com/cancervariants/gene-normalization) DynamoDB tables, which you must download yourself. See the [README](https://github.com/cancervariants/gene-normalization#readme) for deploying the database.
        
        ### Init coding style tests
        
        Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit.
        
        We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
        
        This ensures:
        
        * Check code style
        * Check for added large files
        * Detect AWS Credentials
        * Detect Private Key
        
        Before first commit run:
        
        ```commandline
        pre-commit install
        ```
        
        
        ### Running unit tests
        
        Running unit tests is as easy as pytest.
        
        ```commandline
        pipenv run pytest
        ```
        
Platform: UNKNOWN
Requires-Python: >=3.8
Description-Content-Type: text/markdown
