### Install Tractability Pipeline v2 (Local)

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Installs the Open Targets Tractability Pipeline version 2 from the current directory using pip. This command should be run from the directory containing the setup.py file.

```Shell
pip install .
```

--------------------------------

### Install cx-oracle for Oracle DB

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Installs the cx-oracle Python library, which is a prerequisite if the pipeline needs to connect to an Oracle instance of the ChEMBL database.

```Shell
pip install cx-oracle
```

--------------------------------

### Set CHEMBL_DB Environment Variable (MySQL Example)

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Provides a concrete example of setting the CHEMBL_DB environment variable for connecting to a MySQL instance of the ChEMBL database.

```Environment Variables
CHEMBL_DB=mysql://user:password@host:4233/chembl_30
```

--------------------------------

### Set CHEMBL_DB Environment Variable (Oracle Example)

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Provides an example of setting the CHEMBL_DB environment variable for connecting to an Oracle instance of the ChEMBL database. The full connection string details are omitted in the source.

```Environment Variables
CHEMBL_DB=oracle://...
```

--------------------------------

### Install PROTAC NER Model

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Installs the specific PROTAC Named Entity Recognition (NER) model package required by the pipeline. This command assumes the package file is located within the pipeline's source directory structure.

```Shell
pip install ./ot_tractability_pipeline_v2/en_NER_PROTAC-0.2.5.tar.gz
```

--------------------------------

### Listing Python Dependencies

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/requirements.txt

This snippet lists the Python packages and their specific versions required to run the project. These dependencies are typically installed using pip.

```Python
certifi
chardet==3.0.4
idna==2.8
mygene
numpy>=1.14.3
pandas>=1.0.1
openpyxl
python-dateutil==2.7.3
requests>=2.20.0
six==1.11.0
SQLAlchemy~=1.3.0
urllib3>=1.24.2
spacy>=2.3.2,<3.0.0
mysqlclient
```

--------------------------------

### Run Tractability Pipeline v2

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Executes the Open Targets Tractability Pipeline version 2 using the command-line entry point. It takes a CSV file as input, where the first column contains the Ensembl Gene IDs to be processed.

```Shell
run-ot-pipeline-v2 genes.csv
```

--------------------------------

### Set CHEMBL_DB Environment Variable (Generic)

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Sets the CHEMBL_DB environment variable to define the connection string for the ChEMBL database. This generic format shows the required components: database type, username, password, host, port, and database name.

```Environment Variables
CHEMBL_DB=[DB_TYPE]://[USERNAME]:[PASSWORD]@[HOST]:[PORT]/[DB_NAME]
```

--------------------------------

### Set CHEMBL_VERSION Environment Variable

Source: https://github.com/chembl/tractability_pipeline_v2/blob/master/README.md

Sets the CHEMBL_VERSION environment variable to specify the version of the ChEMBL database the pipeline should use. The pipeline is compatible with ChEMBL version 26 and newer.

```Environment Variables
CHEMBL_VERSION=30
```

=== COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.