### Starting UROPA Query Configuration - JSON

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example.rst

This snippet shows the beginning of the "queries" array within a UROPA configuration JSON. It indicates where individual query objects, defining annotation criteria, will be listed. It's part of setting up how UROPA should annotate genomic peaks.

```JSON
{ "queries":[
```

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

### Install Miniconda Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to run the Miniconda installer script for Linux. This is the first step in setting up the Conda environment for UROPA.

```Bash
bash Miniconda3-latest-Linux-x86_64.sh
```

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

### Source Bioconductor Installer R

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

R command to download and source the `biocLite.R` script, which is used to install packages from the Bioconductor repository.

```R
source("https://bioconductor.org/biocLite.R")
```

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

### Configure UROPA with Feature Anchor and Distance (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example.rst

This JSON configuration demonstrates how to set up UROPA queries using the 'feature.anchor' and 'distance' keys. It defines two queries for 'gene' features, one calculating distance from the feature 'start' and the other from the feature 'center', both with a maximum distance of 5000. It also specifies the input GTF and BED files for annotation.

```json
{
"queries": [
	{"feature":"gene", "distance":5000, "feature.anchor": "start", "show.attributes":"gene_name"},
	{"feature": "gene","distance":5000, "feature.anchor":"center"}],
"priority" : "False",
"gtf": "gencode.v19.annotation.gtf",
"bed": "ENCFF001SUE.bed"
}
```

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

### Example UROPA Configuration File

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/config.rst

This JSON snippet provides a template for the UROPA configuration file. It shows the structure including the mandatory global keys 'queries', 'gtf', and 'bed', as well as the optional 'priority'. It also illustrates the structure of a single query object within the 'queries' array, listing common parameters.

```json
{
    "queries":[
        {"feature":"",    "feature.anchor": "",    "distance":"",    "strand":"",
		"direction":"",    "internals":"",     "filter.attribute":"",
		"attribute.value":"",     "show.attributes":"" }
              ],
    "priority": "",
    "gtf": ".gtf",
    "bed": ".bed"
    }
```

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

### Install UROPA via PyPI

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command installs the UROPA package directly from the Python Package Index (PyPI) using the pip package installer.

```bash
pip install uropa
```

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

### Load devtools Library R

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

R command to load the `devtools` package, which is required for installing packages directly from GitHub.

```R
library(devtools)
```

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

### Running UROPA in a Docker Container (Bash)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/parameter.rst

Provides a bash command example for running the UROPA tool inside a Docker container. It demonstrates how to use the `-v` flag to mount a host directory for input/output files, the `--rm` flag to remove the container after execution, and how to pass UROPA-specific parameters.

```bash
sudo docker run --rm -v <path-to-input-files-on-HOST>:<path-to-container-mnt> UROPA:LATEST uropa <UROPA-Paramters> -p <path-to-container-mnt>/'your-file-prefix'
```

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

### Configuring feature.anchor in UROPA JSON

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example-pdf.rst

This configuration snippet demonstrates how to use the `feature.anchor` key in UROPA queries. It defines two queries for 'gene' features, one using 'start' and the other 'center' as the anchor point for distance calculation. It also sets a maximum distance and specifies input GTF and BED files.

```json
{
"queries": [
	{"feature":"gene", "distance":5000, "feature.anchor": "start", "show.attributes":"gene_name"},
	{"feature": "gene","distance":5000, "feature.anchor":"center"}],
"priority" : "False",
"gtf": "gencode.v19.annotation.gtf",
"bed": "ENCFF001SUE.bed"
}
```

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

### Install UROPA via Pip Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to install the UROPA package from the Python Package Index (PyPI) using pip. Note that this method does not include R dependencies.

```Bash
pip install uropa
```

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

### Install UROPA via Conda Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to install the UROPA package and its Python dependencies within the active Conda environment. This is the recommended installation method.

```Bash
conda install python uropa
```

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

### Install Vennerable from GitHub R

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

R command using `devtools::install_github` to install a modified version of the `Vennerable` package directly from a specified GitHub repository. This is needed for visualizing Chow-Ruskey plots.

```R
install_github("jenzopr/Vennerable")
```

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

### Activate UROPA Conda Environment Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to activate the newly created 'uropa' Conda environment. Subsequent commands will run within this environment.

```Bash
conda activate uropa
```

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

### Install Bioconductor Packages for UROPA R

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

R command using `biocLite` to install specific packages (`RBGL`, `graph`) required by UROPA from the Bioconductor repository.

```R
biocLite(c("RBGL","graph"))
```

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

### Single Query UROPA Configuration

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/output.rst

This JSON snippet shows an example configuration for running UROPA with a single query. It specifies parameters like the target feature ('gene'), maximum distance (10000), anchor point ('start'), filtering criteria ('gene_type' equals 'protein_coding'), and attributes to include in the output ('gene_name', 'gene_type'). This configuration is used to illustrate the 'allhits.txt' and 'finalhits.txt' output files.

```json
{
    "queries":[
            {"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
                "filter.attribute":"gene_type", "attribute.value":"protein_coding",
                "show.attributes":["gene_name","gene_type"]}]
}
```

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

### Configure Uropa with Multiple Queries (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example.rst

This JSON object configures the uropa tool to perform two feature queries: one for 'gene' features within 1000 bp, requesting the 'gene_name' attribute, and another for 'transcript' features within 1000 bp. It disables prioritization and specifies the GTF and BED input files.

```json
{
	"queries":[
		{"feature":"gene", "distance":1000, "show.attributes":"gene_name"},
		{"feature":"transcript", "distance":1000}], 
	"priority" : "False",
	"gtf":"Homo_sapiens.GRCh37.75.gtf",
	"bed":"ENCFF001VFA.bed"
	}
```

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

### Using the uropa2gtf.R Utility

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/custom.rst

Provides examples of command-line usage for the uropa2gtf.R utility, including the basic invocation with just an input file/directory and usage with optional arguments for source, feature, and thread count. The utility converts non-GTF annotation files to GTF format.

```Bash
uropa2gtf.R -i input
```

```Bash
uropa2gtf.R -i input -s yourSource -f yourFeature -t number-threads
```

```Bash
uropa2gtf.R -i wgEncodeAwgTfbsBroadHuvecCtcfUniPk.txt -s ucsc -f tfbs -t 5
```

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

### Add Miniconda to PATH Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to manually add the Miniconda installation directory to the system's PATH environment variable. This allows running conda commands from any terminal location.

```Bash
export PATH=dir/to/miniconda3:$PATH
```

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

### Pull UROPA Docker Image by Tag Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to pull a specific tagged version of the UROPA biocontainer image from Quay.io using Docker. Replace `latest_tag` with the desired version.

```Bash
docker pull quay.io/biocontainers/uropa:latest_tag
```

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

### Install UROPA via Conda

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command installs Python and the UROPA package into the active conda environment, fetching UROPA from the bioconda channel.

```bash
conda install python uropa -c bioconda
```

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

### Create Conda Environment for UROPA Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to create a new isolated Conda environment named 'uropa'. This environment will house the UROPA installation and its dependencies.

```Bash
conda create --name uropa
```

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

### Install CRAN Packages for UROPA R

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

R command to install a list of required packages from the Comprehensive R Archive Network (CRAN). These packages are necessary for UROPA's auxiliary R scripts.

```R
install.packages(c("ggplot2","devtools","gplots","gridExtra","jsonlite", "VennDiagram","snow","getopt","tidyr","UpSetR"))
```

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

### Pull UROPA Docker Image by Name Bash

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/install.rst

Command to pull the latest version of the UROPA Docker image from the loosolab repository. This provides a containerized environment for UROPA.

```Bash
docker pull loosolab/uropa
```

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

### UROPA Configuration without Priority (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example-pdf.rst

This JSON configuration file for UROPA defines two queries: one for genes and one for transcripts, both with a distance threshold of 1000 bp. The 'priority' is set to 'False', indicating that UROPA should evaluate all defined queries for each peak rather than stopping after the first valid annotation is found. It also specifies the GTF and BED input files.

```json
{
	"queries":[
		{"feature":"gene", "distance":1000, "show.attributes":"gene_name"},
		{"feature":"transcript", "distance":1000}], 
	"priority" : "False",
	"gtf":"Homo_sapiens.GRCh37.75.gtf",
	"bed":"ENCFF001VFA.bed"
	}
```

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

### UROPA Configuration with Direction Query

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example.rst

This JSON object defines a UROPA configuration with two queries. The first is a standard gene annotation query, while the second specifically uses the 'direction':'upstream' parameter to annotate peaks located upstream of genes. It also specifies the input GTF and BED files.

```json
{
  "queries": [
  	{"feature": "gene", "distance":1000, "show.attributes":"gene_name"},
  	{"feature": "gene", "distance":1000, "direction":"upstream"}],
  "gtf": "gencode.v19.annotation.gtf",
  "bed": "ENCFF001SUE.bed"
  }
```

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

### Configuring Uropa with Internals Parameter (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example.rst

This JSON configuration demonstrates the use of the 'internals' key in Uropa queries. Query 0 shows the default behavior, while Query 1 sets 'internals' to 'True' to ensure features located within large peaks (or vice versa) are annotated even if the distance exceeds the specified limit. Requires a GTF file ('Homo_sapiens.GRCh37.75.gtf') and a BED file ('ENCFF001VFA.bed').

```json
{
	"queries":[
		{"feature":"gene", "distance":500, "show.attributes":"gene_name"},
		{"feature":"gene", "distance":500, "internals":"True"}],
	"gtf":"Homo_sapiens.GRCh37.75.gtf",
	"bed":"ENCFF001VFA.bed"
	}
```

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

### UROPA Configuration for Multiple Queries (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/output-pdf.rst

Example JSON configuration file used to run UROPA with multiple queries. It defines three distinct queries based on gene type (protein_coding, lincRNA, misc_RNA), specifies the distance threshold, anchor point, internal inclusion, attribute filtering, and attributes to show. It also sets the priority flag to false and specifies the input GTF and BED files.

```json
{
	"queries":[
			{"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
				"filter.attribute":"gene_type",  "attribute.value":"protein_coding",
				"show.attributes":["gene_name","gene_type"]},
			{"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
				"filter.attribute":"gene_type",  "attribute.value":"lincRNA"},
			{"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
				"filter.attribute":"gene_type",  "attribute.value":"misc_RNA"}
			  ],
    "priority" : "False",
    "gtf": "gencode.v19.annotation.gtf",
    "bed": "ENCFF001VFA.peaks.bed"
    }
```

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

### Activate Conda Environment for UROPA

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command activates the previously created conda environment named 'uropa', making its installed packages available in the current shell session.

```bash
conda activate uropa
```

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

### Define Gene Annotation Queries and Inputs (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example.rst

This snippet shows how to define multiple queries for gene annotation. The first query selects 'gene' features within 5000 bp and specifies 'gene_name' and 'gene_biotype' attributes to show. The second query adds a filter to only include 'gene' features where the 'gene_biotype' is 'protein_coding'. It also specifies the input GTF and BED files.

```JSON
		{"feature":"gene", "distance":5000, "show.attributes":["gene_name","gene_biotype"]},
		{"feature":"gene", "distance":5000, "filter.attribute": "gene_biotype", 
			"attribute.value": "protein_coding"}],
		"gtf":"Homo_sapiens.GRCh37.75.gtf",
		"bed":"ENCFF001VFA.bed"
		}
```

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

### UROPA Config: Distance and Directional Queries (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example-pdf.rst

Defines two UROPA queries for peak annotation. The first uses a general distance limit (1000 bp), while the second adds a 'direction' filter ('upstream') within the same limit. Specifies GTF and BED input files. Useful for prioritizing annotations based on biological context.

```json
{
"queries": [
	{"feature": "gene", "distance":1000, "show.attributes":"gene_name"},
	{"feature": "gene", "distance":1000, "direction":"upstream"}],
"gtf": "gencode.v19.annotation.gtf",
"bed": "ENCFF001SUE.bed"
}
```

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

### UROPA Config: Using the 'internals' Key (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/uropa-example-pdf.rst

Compares two UROPA queries with a 500 bp distance limit. The first shows default behavior. The second sets 'internals' to 'True', allowing annotation of features within peaks (or vice versa) even if the distance exceeds the limit. Prevents loss of annotations for large features/peaks.

```json
{
"queries":[
	{"feature":"gene", "distance":500, "show.attributes":"gene_name"},
	{"feature":"gene", "distance":500, "internals":"True"}],
"gtf":"Homo_sapiens.GRCh37.75.gtf",
"bed":"ENCFF001VFA.bed"
}
```

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

### UROPA Configuration for Multiple Queries (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/output.rst

This JSON object defines a configuration for running UROPA with three distinct queries. Each query targets genes within 10kb of their start, filtering by gene type (protein_coding, lincRNA, misc_RNA). It specifies the GTF and BED input files and sets the priority option to False.

```json
{
	"queries":[
            {"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
                "filter.attribute":"gene_type",  "attribute.value":"protein_coding",
                "show.attributes":["gene_name","gene_type"]},
            {"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
                "filter.attribute":"gene_type",  "attribute.value":"lincRNA"},
            {"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
                "filter.attribute":"gene_type",  "attribute.value":"misc_RNA"}
              ],
    "priority" : "False",
    "gtf": "gencode.v19.annotation.gtf",
    "bed": "ENCFF001VFA.peaks.bed"
    }
```

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

### UROPA Single Query Configuration (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/output-pdf.rst

This JSON object defines a sample configuration for UROPA using a single query. It specifies the feature type ("gene"), maximum distance (10000), anchor point ("start"), inclusion of internals, filtering by "gene_type" equal to "protein_coding", attributes to show ("gene_name", "gene_type"), no priority setting, and input GTF and BED files. This configuration is used to illustrate the output tables for a single query scenario.

```json
{
    "queries":[
            {"feature":"gene", "distance":10000, "feature.anchor":"start", "internals":"True", 
                "filter.attribute":"gene_type", "attribute.value":"protein_coding",
                "show.attributes":["gene_name","gene_type"]}], 
     "priority" : "False",
     "gtf":"gencode.v19.annotation.gtf" ,
     "bed":"ENCFF001VFA.bed"
    }
```

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

### Running UROPA with Configuration File (Bash)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/introduction.rst

This command initiates the UROPA peak annotation process. It requires a configuration file in JSON format, specified using the `-i` flag, which defines the annotation parameters and queries. The `<config.json>` placeholder should be replaced with the actual path to the configuration file.

```bash
uropa –i <config.json>
```

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

### Displaying UROPA Help and Usage (Bash)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/introduction.rst

This command displays the help message for the UROPA tool. It provides an overview of the available command-line parameters, options, and general usage instructions, which is useful for understanding how to run the tool and its capabilities.

```bash
uropa --help
```

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

### UROPA Command-line Help

Source: https://github.com/loosolab/uropa/blob/master/README.md

Displays the command-line interface for the UROPA tool, listing all available options for single queries, configuration files, and additional settings like output directory, threads, logging, and debugging.

```bash
$ uropa
Usage: uropa [options]

optional arguments:
  -h, --help                       show this help message and exit

Arguments for one query:
  -b , --bed                       Filename of .bed-file to annotate
  -g , --gtf                       Filename of .gtf-file with features
  --feature [ [ ...]]              Feature for annotation
  --feature_anchor [ [ ...]]       Feature anchor to annotate to
  --distance [ [ ...]]             Maximum permitted distance from feature (1 or 2
                                   arguments)
  --strand [ [ ...]]               Desired strand of annotated feature relative to peak
  --relative_location [ [ ...]]    Peak locaion relative to feature location
  --internals                      Set minimum overlap fraction for internal feature
                                   annotations. 0 equates to internals=False and 1 equates
                                   to internals=True. Default is False.
  --filter_attribute               Filter on 9th column of GTF
  --attribute_values [ [ ...]]     Value(s) of attribute corresponding to
                                   --filter_attribute
  --show_attributes [ [ ...]]      A list of attributes to show in output

Multi-query configuration file:
  -i config.json, --input config.json
                                   Filename of configuration file (keys in this file
                                   overwrite command-line arguments about query)

Additional arguments:
  -p , --prefix                    Prefix for result file names (defaults to basename of
                                   .bed-file)
  -o , --outdir                    Output directory for output files (default: current
                                   dir)
  -s, --summary                    Filename of additional visualisation of results in
                                   graphical format
  -t n, --threads n                Multiprocessed run: n = number of threads to run
                                   annotation process
  -l uropa.log, --log uropa.log    Log file name for messages and warnings (default: log
                                   is written to stdout)
  -d, --debug                      Print verbose messages (for debugging)
  -v, --version                    Prints the version and exits
```

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

### UROPA Command-Line Usage and Parameters (Bash)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/parameter.rst

Shows the general command structure for running UROPA from the command line and lists all available optional arguments. These parameters control input/output files, annotation queries (features, distance, strand, location, filtering), multiprocessing, logging, and version information.

```bash
Usage: uropa [options]

UROPA - Universal RObust Peak Annotator.

optional arguments:
  -h, --help                       show this help message and exit

Arguments for one query:
  -b , --bed                       Filename of .bed-file to annotate
  -g , --gtf                       Filename of .gtf-file with features
  --feature [ [ ...]]              Feature for annotation
  --feature-anchor [ [ ...]]       Specific feature anchor to annotate to
  --distance [ [ ...]]             Maximum permitted distance from feature (1 or 2
				   arguments)
  --strand                         Desired strand of annotated feature relative to peak
  --relative-location [ [ ...]]    Peak location relative to feature location
  --internals                      Set minimum overlap fraction for internal feature
				   annotations. 0 equates to internals=False and 1 equates
				   to internals=True. Default is False.
  --filter-attribute               Filter on 9th column of GTF
  --attribute-values [ [ ...]]     Value(s) of attribute corresponding to --filter-
				   attribute
  --show-attributes [ [ ...]]      A list of attributes to show in output (default: all)

Multi-query configuration file:
  -i config.json, --input config.json
				   Filename of configuration file (keys in this file
				   overwrite command-line arguments about query)

Additional arguments:
  -p , --prefix                    Prefix for result file names (defaults to basename of
				   .bed-file)
  -o , --outdir                    Output directory for output files (default: current
				   dir)
  --output-by-query                Additionally create output files for each named query
				   seperately
  -s, --summary                    Create additional visualisation of results in graphical
				   format
  -t n, --threads n                Multiprocessed run: n = number of threads to run
				   annotation process
  -l uropa.log, --log uropa.log    Log file name for messages and warnings (default: log
				   is written to stdout)
  -d, --debug                      Print verbose messages (for debugging)
  -v, --version                    Prints the version and exits
  -c , --chunk                     Number of lines per chunk for multiprocessing (default:
				   1000)
```

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

### Defining Multiple Queries in Configuration (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/help.rst

Illustrates the structure for defining multiple queries within the configuration file. The 'queries' key should contain an array `[]` where each query is represented by a separate object `{}`. Multiple query objects are separated by commas.

```JSON
"queries":[{},{}]
```

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

### Run UROPA with Configuration File

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command executes UROPA using a specified configuration file ('sample_config.json') and sets the number of threads to 4. This method supports multiple queries defined in the config file.

```bash
uropa -i sample_config.json -t 4
```

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

### Uropa Analysis Configuration (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/output.rst

This JSON snippet shows a basic configuration used to run the Uropa tool. It specifies input files (GTF and BED) and a boolean parameter 'priority'.

```JSON
"priority" : "False",
"gtf":"gencode.v19.annotation.gtf" ,
"bed":"ENCFF001VFA.bed"

```

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

### Run UROPA in Docker Container

Source: https://github.com/loosolab/uropa/blob/master/README.md

Provides the command to execute UROPA within a Docker container using `sudo docker run`. It explains the `-v` parameter for mounting volumes and the `--rm` option, emphasizing the need to use the `-p` option for output.

```bash
sudo docker run --rm -v <path-to-input-files-on-HOST>:<path-to-container-mnt> UROPA:LATEST uropa <UROPA-Paramters> -p <path-to-container-mnt>/'your-file-prefix'
```

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

### Specify Output Attributes (Python)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/config.rst

Lists attributes from the GTF file to include in the final output tables. Non-existent attributes will show 'NA'. Use 'all' to include all possible attributes.

```Python
'show.attributes':['gene_id', 'gene_biotype']
```

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

### Annotating with Default Values Only (JSON)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/help.rst

Shows how to configure UROPA to use only default annotation values. This is achieved by including the 'queries' key in the configuration file but providing an empty array `[]` as its value.

```JSON
"queries":[]
```

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

### Create Conda Environment for UROPA

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command creates a new conda environment named 'uropa'. Conda environments help manage dependencies and isolate projects.

```bash
conda create --name uropa
```

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

### Run UROPA with BED and GTF Files

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command runs UROPA directly using input genomic regions from a BED file ('test_data/genomic_regions.bed') and a reference annotation from a GTF file ('test_data/gencode.v29.annotation.chr19.gtf'). This direct method supports only a single query.

```bash
uropa --bed test_data/genomic_regions.bed --gtf test_data/gencode.v29.annotation.chr19.gtf
```

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

### Pull UROPA Docker Image

Source: https://github.com/loosolab/uropa/blob/master/README.md

This command pulls the latest available UROPA container image from the Biocontainers repository on Quay.io using Docker.

```bash
docker pull quay.io/biocontainers/uropa:latest_tag
```

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

### Set Query Priority (Python)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/config.rst

Determines if queries are treated hierarchically ('Yes') or equally ('False'). If 'Yes', a peak is annotated by a query only if no match is found for preceding queries.

```Python
'priority':'Yes'
```

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

### Configure Attribute Value Filter (Python)

Source: https://github.com/loosolab/uropa/blob/master/docs_rst/config.rst

Sets the required value(s) for the attribute specified by 'filter.attribute'. Only features matching these values will be considered valid annotations. Defaults to 'None'.

```Python
'attribute.value': ['protein_coding']
```

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