### Install Ephemeris with Pip

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/installation.rst

Installs or upgrades Ephemeris using pip. This includes a traditional installation, upgrading an existing installation, and installing from the development branch.

```bash
$ virtualenv .venv; . .venv/bin/activate
$ pip install ephemeris
```

```bash
$ . .venv/bin/activate
$ pip install -U ephemeris
```

```bash
$ pip install -U git+git://github.com/galaxyproject/ephemeris.git
```

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

### Install Galaxy Tools with shed-tools install

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Installs Galaxy tools from a Tool Shed using a YAML configuration file. Requires Galaxy instance URL, API key, and a tool list file. Outputs installation logs. The tool list YAML defines tools by name, owner, revisions, and optional section labels.

```bash
# Install tools from a YAML file
shed-tools install \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --tool_list_file tool_list.yaml \
  --log_file installation.log

# Tool list YAML format
# tools:
# - name: 'bwa'
#   owner: 'devteam'
#   tool_panel_section_label: 'NGS mapping'
#   revisions:
#   - '051eba708f43'
#   install_resolver_dependencies: True
```

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

### Install Galaxy Repositories with Ephemeris

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Installs Galaxy repositories using the ephemeris library. It handles repository installation, dependency resolution, and provides counts of installed, skipped, and errored repositories.

```python
from ephemeris import irm

results = irm.install_repositories(
    repositories=repos,
    force_latest_revision=False,
    default_install_resolver_dependencies=True
)

print(f"Installed: {len(results.installed_repositories)}")
print(f"Skipped: {len(results.skipped_repositories)}")
print(f"Errored: {len(results.errored_repositories)}")
```

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

### Install Sphinx for Documentation

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

This command installs Sphinx and its dependencies from the docs/requirements.txt file, necessary for building the project's documentation locally.

```shell
pip install -r docs/requirements.txt
```

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

### Install Ephemeris with Conda

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/installation.rst

Installs Ephemeris using Conda. It requires adding the bioconda channel and then installing the package.

```bash
$ conda config --add channels bioconda
$ conda install ephemeris
```

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

### Setup Galaxy Data Libraries with setup-data-libraries CLI

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Creates and populates Galaxy data libraries using a YAML configuration file. Supports data sources from URLs or local paths, and has a '--training' flag for specific configurations.

```bash
# Setup data library from YAML
setup-data-libraries \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --infile library_data.yaml \
  --training

# Library YAML format:
# destination:
#   type: library
#   name: "Training Data"
#   description: "Reference datasets for training"
# items:
#   - name: "Test Folder"
#     items:
#       - url: https://example.com/data.fasta
#         src: url
#         ext: fasta
#         dbkey: "hg38"
```

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

### Programmatic Tool Repository Installation with Python

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Programmatically install and manage Galaxy tool repositories using the `InstallRepositoryManager` class. Allows fine-grained control over installations by defining repositories with details like name, owner, Tool Shed URL, panel section, and changeset revision.

```python
from bioblend.galaxy import GalaxyInstance
from ephemeris.shed_tools import InstallRepositoryManager

# Connect to Galaxy
gi = GalaxyInstance(url='http://localhost:8080', key='your-api-key')
irm = InstallRepositoryManager(gi)

# Define repositories to install
repos = [
    {
        'name': 'bwa',
        'owner': 'devteam',
        'tool_shed_url': 'https://toolshed.g2.bx.psu.edu',
        'tool_panel_section_label': 'NGS Tools',
        'changeset_revision': '051eba708f43'
    }
]
```

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

### Set up Virtual Environment for Ephemeris

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

This command sets up a virtual environment for local development of the Ephemeris project, assuming you have virtualenvwrapper installed.

```shell
make setup-venv
```

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

### Install Tool Dependencies with install-tool-deps CLI

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Installs tool dependencies for tools already present in a Galaxy instance. Can be used to install dependencies for all tools or for specific tools identified by name and owner.

```bash
# Install dependencies for all tools
install-tool-deps \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here

# Install dependencies for specific tools
install-tool-deps \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --name bwa \
  --owner devteam
```

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

### Test Galaxy Tools with shed-tools test

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Runs automated tests for installed Galaxy tools and generates a JSON test report. Supports testing tools from a list or all installed tools, with options for parallel execution. Requires Galaxy instance URL, API key, and a tool list file.

```bash
# Test tools from a tool list
shed-tools test \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --tool_list_file tool_list.yaml \
  --test_json test_results.json \
  --parallel_tests 4

# Test all installed tools
shed-tools test \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --test_json all_tools_results.json \
  --parallel_tests 2
```

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

### Generate Tool List YAML from Workflows with workflow-to-tools CLI

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Generates a tool list YAML file from Galaxy workflow files, specifying required tools. This output can then be used with shed-tools to install the extracted tools.

```bash
# Extract tools from workflows
workflow-to-tools \
  --workflow workflow1.ga workflow2.ga workflow3.ga \
  --output_file required_tools.yaml \
  --panel_label "Workflow Tools"

# Then install the extracted tools
shed-tools install \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --tool_list_file required_tools.yaml
```

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

### Export Galaxy Tool List with get-tool-list

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Exports a list of currently installed Galaxy tools to a YAML file, useful for backup or replication. Options include exporting all tools with revisions or including tool panel IDs and data managers. Requires Galaxy instance URL and API key.

```bash
# Export all tools with revisions
get-tool-list \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --output_file installed_tools.yaml \
  --get_all_tools

# Export with tool panel IDs
get-tool-list \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --output_file tools_with_sections.yaml \
  --include_tool_panel_id \
  --get_data_managers
```

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

### Run Galaxy Data Managers with run-data-managers

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Executes Galaxy data managers to provision reference genomes and index files using a configuration YAML file. Requires Galaxy instance URL, API key, and a configuration file. Outputs installation logs. The config YAML specifies data manager IDs, parameters, items, and data table reloads.

```bash
# Run data managers from configuration
run-data-managers \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --config data_managers.yaml \
  --log_file dm_installation.log

# Configuration YAML format:
data_managers:
  - id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.2
    params:
      - 'dbkey_source|dbkey': '{{ item }}'
      - 'reference_source|reference_source_selector': 'ucsc'
    items:
      - hg38
      - mm10
    data_table_reload:
      - all_fasta
      - __dbkeys__
```

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

### Get Authenticated Galaxy Connection with ephemeris

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Creates an authenticated Galaxy connection object using the ephemeris library. It can parse arguments or read from a YAML configuration file for connection details.

```python
from ephemeris import get_galaxy_connection
import argparse

# Parse arguments
parser = argparse.ArgumentParser()
parser.add_argument('--galaxy', default='http://localhost:8080')
parser.add_argument('--api_key', default=None)
args = parser.parse_args()

# Connect to Galaxy (tries API key, then username/password, then env var)
gi = get_galaxy_connection(args, file='config.yaml', login_required=True)

# Use the connection
version = gi.config.get_version()
print(f"Connected to Galaxy {version['version_major']}")
```

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

### Update Galaxy Tools with shed-tools update

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Updates installed Galaxy tools to their latest revisions. Can update all tools or specific tools listed in a YAML file. Requires Galaxy instance URL and API key.

```bash
# Update all installed tools
shed-tools update \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here

# Update specific tools from a list
shed-tools update \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --tool_list_file tools_to_update.yaml
```

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

### Wait for Galaxy Instance with Verbose Output (Shell)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/commands/galaxy-wait.rst

This example shows how to use the verbose option ('-v') with galaxy-wait. When enabled, it prints logging statements indicating the progress of the check, including connection attempts and retry messages. This is useful for debugging or monitoring the waiting process.

```shell
$ galaxy-wait -g http://localhost:8080 -v
```

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

### Handling Non-JSON Response Error (Shell)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/commands/galaxy-wait.rst

This example demonstrates the error handling when galaxy-wait receives non-JSON content from the Galaxy instance. The traceback indicates a 'JSONDecodeError', which occurs because the tool expects a JSON response from the '/api/version' endpoint. If the host returns HTML or other non-JSON data, this error will be raised.

```shell
$ galaxy-wait -g https://example.com -v --timeout 3
```

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

### Configure PyPI Credentials (.pypirc)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/developing.rst

This configuration snippet shows the structure of the ~/.pypirc file, which is necessary for interacting with PyPI (Python Package Index) for releasing packages. It includes settings for both the production and test PyPI servers, requiring username and password for authentication.

```ini
[distutils]
index-servers =
    pypi
    test

[pypi]
username:<username>
password:<password>

[test]
repository:https://testpypi.python.org/pypi
username:<username>
password:<password>
```

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

### Open Project Documentation (Makefile)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/developing.rst

This command opens the locally built documentation for the Ephemeris project. It is used to review the changelog and ensure the documentation is accurate before a release.

```bash
make open-docs
```

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

### Automate Full Release Process (Makefile)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/developing.rst

This command executes the complete release process for Ephemeris. It automates pushing packages to a test PyPI, allows for review, publishes to the production PyPI, tags the git repository, and pushes the tag upstream.

```bash
make release
```

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

### Clean, Lint, and Test Project (Makefile)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/developing.rst

This command performs essential development tasks: cleaning build artifacts, linting the code for style and quality, and running unit tests to ensure correctness. It's a crucial step before initiating a release.

```bash
make clean && make lint && make test
```

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

### Build HTML Documentation

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

This command, executed from the docs directory, builds the HTML documentation for Ephemeris. This is useful for previewing documentation changes before submitting a pull request.

```shell
make html
```

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

### Execute Local Release Build (Makefile)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/developing.rst

This command initiates a local build process for releasing packages. It's a step in the larger release automation, allowing for local review before pushing to a remote repository.

```bash
make release-local
```

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

### Wait for Galaxy Instance with galaxy-wait CLI

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Blocks until a Galaxy instance is responsive, useful for Docker and CI/CD pipelines. Supports timeouts and ensuring the API key is valid and belongs to an admin user.

```bash
# Wait for Galaxy to start (no timeout)
galaxy-wait --galaxy http://localhost:8080

# Wait with timeout
galaxy-wait \
  --galaxy http://localhost:8080 \
  --timeout 300

# Wait until API key is valid and user is admin
galaxy-wait \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --ensure_admin

# Returns exit code 0 on success, 1 on failure/timeout
```

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

### Import Galaxy Workflows with workflow-install CLI

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Imports Galaxy workflow files (.ga format) into a Galaxy instance. Supports importing single workflows or all workflows from a directory, with an option to publish them. Deduplicates by UUID.

```bash
# Import a single workflow
workflow-install \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --workflow_path my_workflow.ga

# Import all workflows from a directory
workflow-install \
  --galaxy http://localhost:8080 \
  --api_key your-api-key-here \
  --workflow_path ./workflows/ \
  --publish_workflows

# Workflows are deduplicated by UUID - existing workflows won't be re-imported
```

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

### Push Release Artifacts (Makefile)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/developing.rst

This command is used to push the release artifacts, likely built locally, to a repository. It is part of the multi-step release process for Ephemeris.

```bash
make push-release
```

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

### Clone Ephemeris Repository

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

This command clones your forked Ephemeris repository to your local machine. Ensure you replace 'your_name_here' with your GitHub username.

```shell
git clone git@github.com:your_name_here/ephemeris.git
```

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

### Commit and Push Ephemeris Changes

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

This sequence of commands stages all your changes, commits them with a descriptive message, and pushes your branch to GitHub. Replace 'Your detailed description of your changes.' with a clear summary of your modifications.

```shell
git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature
```

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

### Lint and Test Ephemeris Changes

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

These commands are used to check your local changes for code quality issues using flake8 and run the project's tests. Ensure your contributions adhere to the project's standards.

```shell
make lint
```

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

### Programmatic Data Manager Execution with Python

Source: https://context7.com/galaxyproject/ephemeris/llms.txt

Programmatically manage Galaxy data manager execution using the `DataManagers` class from the Ephemeris library. Connects to Galaxy via BioBlend, loads configuration from a YAML file, and runs data managers with options for logging, error handling, and overwrite behavior.

```python
from bioblend.galaxy import GalaxyInstance
from ephemeris import load_yaml_file
from ephemeris.run_data_managers import DataManagers

# Connect to Galaxy
gi = GalaxyInstance(url='http://localhost:8080', key='your-api-key')

# Load configuration
config = load_yaml_file('data_managers.yaml')

# Initialize and run data managers
dm = DataManagers(gi, config)
results = dm.run(
    log=None,
    ignore_errors=False,
    overwrite=False,
    data_manager_mode='populate',
    history_name='Reference Data Installation'
)

print(f"Successful: {len(results.successful_jobs)}")
print(f"Failed: {len(results.failed_jobs)}")
print(f"Skipped: {len(results.skipped_jobs)}")
```

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

### Wait for Galaxy Instance (Shell)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/commands/galaxy-wait.rst

This command-line snippet demonstrates how to use galaxy-wait to poll a Galaxy instance. The '-g' flag specifies the Galaxy URL. The tool will repeatedly check for availability until the instance responds successfully or the timeout is reached. It's designed to exit with a status code of 0 on success.

```shell
$ galaxy-wait -g https://fqdn/galaxy
```

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

### Create a New Branch for Development

Source: https://github.com/galaxyproject/ephemeris/blob/master/CONTRIBUTING.rst

This command creates a new branch for your bug fix or feature development. Replace 'name-of-your-bugfix-or-feature' with a descriptive name for your branch.

```shell
git checkout -b name-of-your-bugfix-or-feature
```

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

### Wait for Galaxy Instance with Timeout (Shell)

Source: https://github.com/galaxyproject/ephemeris/blob/master/docs/commands/galaxy-wait.rst

This snippet illustrates using the '--timeout' option with galaxy-wait. By default, the tool waits indefinitely. Setting a timeout (e.g., '--timeout 3' for 3 seconds) will cause galaxy-wait to exit with an error code (1) if the Galaxy instance doesn't become available within the specified duration.

```shell
$ galaxy-wait -g https://does-not-exist -v --timeout 3
```

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