Galaxy

https://github.com/galaxyproject/galaxy
Admin
Galaxy is an open, web-based platform for data integration, analysis, and publication, primarily...
Tokens:434,174
Snippets:3,741
Trust Score:9.9
License:MIT
Update:2 weeks ago
Show doc for...
Tokens:
Raw
### Install dependencies and build the library

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/packages/api-client/README.md

Install dependencies, build the library for distribution, and run watch mode for development.

```bash
npm install
```

```bash
npm run build
```

```bash
npm run dev
```

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

### Start Galaxy with run.sh

Source: https://github.com/galaxyproject/galaxy/blob/dev/README.rst

Starts the Galaxy server. After startup completes, Galaxy is available at http://localhost:8080.

```console
$ sh run.sh
```

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

### MySQL connection string example

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/production.md

Example connection string for MySQL, which is currently unsupported and may require troubleshooting. Set this as `database_connection` in `config/galaxy.yml`.

```default
mysql://username:password@localhost/mydatabase
```

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

### Start Tool Shed backend

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/README.md

Run from the galaxy root directory to start the Tool Shed backend, required for local development.

```shell
./run_tool_shed.sh
```

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

### Install Galaxy API Client with npm

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/packages/api-client/README.md

Install the standalone Galaxy API client library using npm.

```bash
npm install @galaxyproject/galaxy-api-client
```

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

### Initialize Galaxy configuration file

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/production.md

Copy the sample configuration file to config/galaxy.yml before starting the server. Changes to this file require a server restart to take effect.

```bash
cp config/galaxy.yml.sample config/galaxy.yml
```

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

### Start Galaxy in the background with galaxyctl start

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/scaling.md

After activating Galaxy's virtual environment, use `galaxyctl start` to start Galaxy in the background. The output shows the status of celery, celery-beat, and gunicorn processes, and indicates where log files are stored.

```console
$ galaxyctl start
celery                           STARTING
celery-beat                      STARTING
gunicorn                         STARTING
Log files are in /Users/mvandenb/src/doc_test/database/gravity/log
```

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

### Start HMR dev server

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/README.md

Starts the Vite dev server with hot module replacement for frontend development.

```shell
pnpm dev
```

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

### Start standalone Galaxy handlers with galaxy-main

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/scaling.md

Use these commands when not using run.sh or the generated supervisor setup to start webless handler processes. Each handler needs a distinct --server-name that must match the handler IDs in job_conf.xml for statically defined handlers. Avoid setting a common server_name in the shared galaxy.yml or exporting the Gunicorn server-name environment setting, as configuration values can override command-line names.

```console
$ cd /srv/galaxy/server
$ ./scripts/galaxy-main -c config/galaxy.yml --server-name handler0 --daemonize
$ ./scripts/galaxy-main -c config/galaxy.yml --server-name handler1 --daemonize
$ ./scripts/galaxy-main -c config/galaxy.yml --server-name handler2 --daemonize
```

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

### Example CLI tool: dump_tour.py

Source: https://github.com/galaxyproject/galaxy/blob/dev/packages/selenium/README.rst

Complete example of a CLI automation tool using the galaxy.selenium.cli module. Demonstrates argument parsing, DriverWrapper creation, and a callback for tour steps.

```python
#!/usr/bin/env python
import argparse
from galaxy.selenium import cli

def main(argv=None):
    args = _arg_parser().parse_args(argv)
    driver_wrapper = cli.DriverWrapper(args)

    # Use driver_wrapper for automation
    callback = DumpTourCallback(driver_wrapper, args.output)
    driver_wrapper.run_tour(args.tour, tour_callback=callback)

def _arg_parser():
    parser = argparse.ArgumentParser(description="Walk a Galaxy tour")
    parser.add_argument("tour", help="tour to walk")
    parser.add_argument("-o", "--output", help="screenshot output dir")
    parser = cli.add_selenium_arguments(parser)  # Add standard args
    return parser

class DumpTourCallback:
    def handle_step(self, step, step_index: int):
        self.driver_wrapper.save_screenshot(f"{output}/{step_index}.png")
```

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

### Install pbs_python for PBS runner

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/cluster.md

Required setup for the PBS job runner. pbs_python must be compiled against your TORQUE installation, so it cannot be provided with Galaxy. Run these commands as the Galaxy user.

```console
galaxy_user@galaxy_server% git clone https://github.com/ehiggs/pbs-python
galaxy_user@galaxy_server% cd pbs-python
galaxy_user@galaxy_server% source /clusterfs/galaxy/galaxy-app/.venv/bin/activate
galaxy_user@galaxy_server% python setup.py install
```

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

### API Call with openapi-fetch

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Example of using the typed client from ToolShedApi() to fetch repositories with query parameters.

```typescript
import { ToolShedApi } from "@/schema"
const { data } = await ToolShedApi().GET("/api/repositories", { params: { query: params } })
```

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

### Run tests

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/packages/api-client/README.md

Run the vitest tests as a sanity check. Use watch mode during development.

```bash
npm test
```

```bash
npm run test:watch
```

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

### Run local Tool Shed with dev overrides

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/README.md

Starts a local Tool Shed with rapid bootstrapping and Vite dev server mode. Uses TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY, TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV, and TOOL_SHED_VITE_PORT=4040.

```shell
TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 TOOL_SHED_VITE_PORT=4040 ./run_tool_shed.sh
```

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

### Enable and start Galaxy with systemctl

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/scaling.md

Command to enable and start the Galaxy systemd service. The output shows the symlink created for the service.

```console
# systemctl enable galaxy
Created symlink from /etc/systemd/system/multi-user.target.wants/galaxy.service to /etc/systemd/system/galaxy.service.
```

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

### Example test using provides_repositories fixture

Source: https://github.com/galaxyproject/galaxy/blob/dev/test/unit/tool_shed/README.md

Shows how to use the provides_repositories fixture for repository operations. The example uploads the 'column_maker' directory from test_data/repos/ and expects 3 downloadable revisions.

```python
def test_upload(provides_repositories, new_repository):
    upload_directories_to_repository(
        provides_repositories,
        new_repository,
        "column_maker"  # From test_data/repos/
    )
    assert len(new_repository.downloadable_revisions) == 3
```

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

### ascp file source plugin configuration for EBI SRA downloads

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/data.md

Example YAML configuration for the ascp plugin, which provides high-speed downloads via the Aspera FASP protocol. Requires the ascp binary installed on the Galaxy server. The plugin is download-only, supports ascp:// and fasp:// URLs, and requires SSH key content embedded directly (not file paths) because Galaxy jobs may not mount configuration directories. It is not browsable or writable.

```yaml
- type: ascp
  id: ebi_aspera
  label: "EBI Aspera Downloads"
  doc: "High-speed downloads from EBI SRA using Aspera FASP protocol"
  ascp_path: "ascp" # Path to ascp binary
  user: "era-fasp"
  host: "fasp.sra.ebi.ac.uk"
  port: 33001
  rate_limit: "300m" # Transfer rate limit (e.g., "300m" for 300 Mbps)
  disable_encryption: true # Disable encryption for maximum speed
  # Retry and resume configuration (optional)
  max_retries: 3
  retry_base_delay: 2.0
  retry_max_delay: 60.0
  enable_resume: true
  # SSH key content (required) - embed the key directly in the configuration
  ssh_key_content: |
    -----BEGIN RSA PRIVATE KEY-----
    <YOUR ACTUAL SSH PRIVATE KEY CONTENT>
    -----END RSA PRIVATE KEY-----
  # SSH key passphrase. https://embl.service-now.com/kb?id=kb_article_view&sys_kb_id=4cc60cf8c398a610bf313dfc0501314c#mcetoc_1idpn4k0to
  ssh_key_passphrase: sample_passphrase

```

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

### Run client dev server with pnpm

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Starts the client development server using the package scripts from the client directory.

```bash
pnpm run develop
```

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

### Test file structure example

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Shows the recommended directory structure for test files, placed adjacent to the code they test with .test.ts or .test.js extension.

```text
src/components/MyComponent/
├── MyComponent.vue
├── MyComponent.test.ts
└── test-utils.ts        # optional: shared test utilities
```

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

### Use NavigatesGalaxy API methods

Source: https://github.com/galaxyproject/galaxy/blob/dev/packages/selenium/README.rst

Example of using the NavigatesGalaxy methods available on the driver_wrapper for navigation and element interaction.

```python
# driver_wrapper has all NavigatesGalaxy methods
driver_wrapper.navigate_to(url)
driver_wrapper.click_selector("#my-button")
driver_wrapper.wait_for_selector_visible(".result")
```

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

### Quick start functional tests

Source: https://github.com/galaxyproject/galaxy/blob/dev/packages/tool_shed/CLAUDE.md

Two-terminal workflow: start the shed with ./run_tool_shed.sh, then run functional tests with uv run pytest.

```shell
# Terminal 1: Start shed
./run_tool_shed.sh

# Terminal 2: Run tests
uv run pytest tool_shed/test/functional/test_frontend_login.py -v
```

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

### Test Options API components through template

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Shows good and bad examples: the good test checks the rendered text from a prop, while the bad test accesses wrapper.vm directly.

```typescript
// ✅ Good: Tests through template
test("shows message prop", () => {
    const wrapper = mount(MyComponent, {
        props: { message: "Hello" },
    })
    expect(wrapper.text()).toContain("Hello")
})

// ❌ Avoid: Direct vm access
expect(wrapper.vm.message).toBe("Hello")
```

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

### Example blocklist file format

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/authentication.md

Each domain is listed on its own line without the '@' sign. Domains in this file are blocked during registration.

```default
drdrb.com
mailinator.com
sogetthis.com
spamgourmet.com
trashmail.net
```

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

### db_dev.sh version output example

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/db_migration.md

Example output from the version command showing head revisions for both branches.

```default
$ .db_dev.sh version
186d4835587b (gxy) (head)
d4a650f47a3c (tsi) (head)
```

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

### JavaScript Spacing: Between Scopes and Other Code

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of adding empty lines between a constant definition, an if block, and a console.log call. The 'Do' example includes the blank lines; the 'Don't' example omits them.

```js
const myConstant = 5;

if (myConstant === 5) {
    // do stuff...
}

console.log("log stuff");
```

```js
const myConstant = 5;
if (myConstant === 5) {
    // do stuff...
}
console.log("log stuff");
```

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

### Component Showcase Pattern

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Add reusable UI components to the showcase page at /showcase using this pattern. Wrap each component in <component-showcase> and provide examples with <component-showcase-example> to demonstrate default and prop variations.

```Vue
<component-showcase title="MyComponent">
    <component-showcase-example title="default">
        <my-component />
    </component-showcase-example>
    <component-showcase-example title="with props">
        <my-component some-prop="value" />
    </component-showcase-example>
</component-showcase>
```

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

### db_dev.sh dbversion output example

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/db_migration.md

Example output from the dbversion command. The current revision is marked with `(head)` if it matches the codebase head.

```default
$ ./db_dev.sh dbversion
INFO:alembic.runtime.migration:Context impl PostgresqlImpl.
INFO:alembic.runtime.migration:Will assume transactional DDL.
d4a650f47a3c (head)
6a67bf27e6a6
```

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

### JavaScript Spacing: Variable Definitions and Code

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of adding an empty line between variable definitions and other code. The 'Do' example includes the empty line; the 'Don't' example omits it.

```js
let a = 5;
let b = 6;

console.log(a + b);
```

```js
let a = 5;
let b = 6;
console.log(a + b);
```

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

### Create and activate a virtualenv with virtualenv

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/framework_dependencies.rst

Manually create a virtualenv at /srv/galaxy/venv and activate it. The output shows the new Python executable and installed packages. After activation, the prompt changes to (venv)$.

```console
$ virtualenv /srv/galaxy/venv
New python executable in /srv/galaxy/venv/bin/python
Installing setuptools, pip, wheel...done.
$ . /srv/galaxy/venv/bin/activate
(venv)$
```

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

### Pinia Store Testing Setup for Components

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Sets up a testing Pinia with spies and stubActions false, then mounts a component and accesses the store to set state.

```typescript
import { createTestingPinia } from "@pinia/testing";
import { setActivePinia } from "pinia";

const pinia = createTestingPinia({ createSpy: vi.fn, stubActions: false });
setActivePinia(pinia);

const wrapper = shallowMount(MyComponent, { localVue, pinia });

// Access and manipulate stores
const userStore = useUserStore();
userStore.currentUser = getFakeRegisteredUser();
```

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

### Install Apache on EL

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/apache.md

Install Apache on RedHat Enterprise Linux-based distributions using yum.

```shell-session
# yum install httpd
```

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

### sample_tool_conf.xml example structure

Source: https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/CLAUDE.md

Example structure for the tool configuration file that registers functional test tools with Galaxy. Every test tool must be listed here to be loaded during testing. Paths are relative to test/functional/tools/ and tools can be organized in <section> tags. Both XML and YAML tools are supported.

```xml
<?xml version="1.0"?>
<toolbox tool_path="${tool_conf_dir}">
  <tool file="simple_constructs.xml" />
  <tool file="collection_creates_pair.xml" />
  <tool file="collection_creates_pair_user.yml" />
  <section id="test" name="Test Section">
    <tool file="parameters/gx_boolean.xml" />
    <tool file="parameters/gx_boolean_user.yml" />
  </section>
</toolbox>
```

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

### Example test using new_repository fixture

Source: https://github.com/galaxyproject/galaxy/blob/dev/test/unit/tool_shed/README.md

Shows how to use the new_repository fixture, which creates an empty repository. The fixture is defined in conftest.py.

```python
def test_repo(new_repository):
    assert new_repository.name
    assert len(new_repository.downloadable_revisions) == 0
```

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

### JavaScript Spacing: Between Scopes

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of adding empty lines between function scopes. The 'Do' example includes blank lines between functions and between if blocks; the 'Don't' example omits them.

```js
function myFunction(parameter) {
    if (condition) {
        // do stuff...
    }

    if (otherCondition) {
        // do more stuff...
    }
}

function otherFunction() {
    // do other stuff...
}
```

```js
function myFunction(parameter) {
    if (condition) {
        // do stuff...
    }
    if (otherCondition) {
        // do more stuff...
    }
}
function otherFunction() {
    // do other stuff...
}
```

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

### Install containers from a list file with --container-list

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/special_topics/mulled_containers.rst

Uses the `--container-list` option to install many containers from a file. The file (`list.txt`) should contain one container name per line.

```bash
$ mulled-update-singularity-containers --container-list list.txt --filepath /tmp/sing/ --installation /usr/local/bin/singularity
```

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

### Navigate to Galaxy home page

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy_test/selenium/jupyter/notebook_example_library.ipynb

Calls the home() method on the Galaxy Selenium context to navigate to the Galaxy home page.

```python
gx_selenium_context.home()
```

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

### Multiple Conda Resolvers Example

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst

Example configuration with two conda resolvers: first an administrator-maintained read-only installation at /hpc/conda with auto_init and auto_install disabled, then a Galaxy-maintained writable installation at /galaxy/conda with auto_init and auto_install enabled so missing dependencies are installed at tool runtime.

```yaml
- type: conda
  auto_init: false
  auto_install: false
  prefix: /hpc/conda
- type: conda
  auto_init: true
  auto_install: true
  prefix: /galaxy/conda
```

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

### Command Line Options: python scripts/tool_source/populate_store.py --help

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/tool_source_storage.rst

Shows all command line options for the populate_store.py script. Key options include --config (required), --dry-run, --incremental (default), --full, --tool-id, --parallel (default 4), --rebuild-index, --target, --verbose, --watch, and --watch-polling. Every non-dry-run invocation refreshes the manifest beside each writable file-backed SQLite store it updates; non-SQLite and in-memory stores are skipped.

```console
$ python scripts/tool_source/populate_store.py --help

Options:
  --config, -c PATH      Galaxy configuration file (required)
  --dry-run              Show what would be stored without storing
  --incremental          Only store new/changed tools (default)
  --full                 Force re-store of all tools
  --tool-id PATTERN      Only process tools whose ID contains PATTERN
  --parallel, -j N       Number of parallel workers (default: 4)
  --rebuild-index        Rebuild the tool index after population
  --target NAME          Restrict to a single named store from
                         tool_source_stores (or '__default__'). Without
                         this, every writable store is populated.
  --verbose, -v          Verbose output
  --watch, -w            Watch tool directories and send reload notifications
  --watch-polling        Use polling observer (for NFS/CVMFS/network FS)
```

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

### Vue Template Spacing: Between Logical Blocks

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of adding space between logical blocks of elements. The 'Do' example includes a blank line between the two conditional blocks; the 'Don't' example omits it.

```vue
<div>
    <span v-if="conditional">
        condition 1 met
    </span>
    <span v-else>
        condition 1 not met
    </span>

    <span v-if="otherConditional">
        condition 2 met
    </span>
    <span v-else>
        condition 2 not met
    </span>
</div>
```

```vue
<div>
    <span v-if="conditional">
        condition 1 met
    </span>
    <span v-else>
        condition 1 not met
    </span>
    <span v-if="otherConditional">
        condition 2 met
    </span>
    <span v-else>
        condition 2 not met
    </span>
</div>
```

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

### Domain-specific factory example

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Create domain-specific factories for complex test data, as shown with createFakeHistory.

```typescript
// In test-utils.ts or inline
function createFakeHistory(overrides = {}) {
    return {
        id: "history-id",
        name: "Test History",
        deleted: false,
        ...overrides,
    };
}
```

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

### Install dependencies with common_startup.sh --no-create-venv

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/framework_dependencies.rst

Run common_startup.sh with --no-create-venv to install Galaxy pip and dependencies without creating a virtualenv. The PYTHONPATH is explicitly unset to avoid interference; if problems occur, try unsetting $PYTHONPATH as shown.

```console
(venv)$ PYTHONPATH= sh /srv/galaxy/server/scripts/common_startup.sh --no-create-venv
```

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

### Build Documentation with make docs

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/index.rst

Run from the Galaxy root directory to generate the documentation. Output is placed in doc/build/html/ and requires Sphinx and other dependencies listed in the Makefile.

```default
$ make docs
```

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

### Example test for metadata reset

Source: https://github.com/galaxyproject/galaxy/blob/dev/test/unit/tool_shed/README.md

Complete example test that uploads test data, then resets all metadata on a repository using RepositoryMetadataManager. It expects 3 downloadable revisions before and after the reset.

```python
from tool_shed.context import ProvidesRepositoriesContext
from tool_shed.metadata import repository_metadata_manager
from tool_shed.webapp.model import Repository
from ._util import upload_directories_to_repository


def test_reset_metadata(
    provides_repositories: ProvidesRepositoriesContext,
    new_repository: Repository
):
    # Upload test data
    upload_directories_to_repository(
        provides_repositories,
        new_repository,
        "column_maker"
    )
    assert len(new_repository.downloadable_revisions) == 3

    # Test metadata reset
    rmm = repository_metadata_manager.RepositoryMetadataManager(
        provides_repositories,
        repository=new_repository,
        resetting_all_metadata_on_repository=True,
        updating_installed_repository=False,
        persist=False,
    )
    repo_path = new_repository.repo_path(app=provides_repositories.app)
    rmm.reset_all_metadata_on_repository_in_tool_shed(
        repository_clone_url=repo_path
    )
    assert len(new_repository.downloadable_revisions) == 3
```

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

### Example values for the value column in huggingface.loc

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/data_tables.md

These are example entries for the 'value' column (column 0) in the huggingface.loc file. Use the Hugging Face model ID directly, appending the version if the same model is registered at more than one version. Values must be globally unique across all rows.

```default
black-forest-labs/FLUX.1-dev
sentence-transformers/all-MiniLM-L6-v2
openai/whisper-large-v3_3.0
```

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

### Example test using new_user fixture

Source: https://github.com/galaxyproject/galaxy/blob/dev/test/unit/tool_shed/README.md

Shows how to use the new_user fixture, which creates a random test user. The fixture is defined in conftest.py.

```python
def test_with_user(new_user):
    assert new_user.username
    assert new_user.email
```

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

### env.sh Example Adding bedtools to PATH

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst

An env.sh script that adds a manually installed bedtools installation to the tool execution PATH. It is sourced before running the tool when found in the package version directory.

```bash
#!/bin/sh

export PATH=$PATH:/opt/biosoftware/bedtools/2.20.1/bin
```

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

### Starting webless handlers with galaxy-main

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/scaling.md

Command-line startup for webless handler processes when not using run.sh or supervisor config. Uses --attach-to-pool to assign handlers to pools; handler_0, handler_1, and handler_3 handle unassigned tool executions, while special_0 handles the special tag.

```console
$ cd /srv/galaxy/server
./scripts/galaxy-main -c config/galaxy.yml --server-name handler_0 --attach-to-pool job-handlers --attach-to-pool workflow-scheduler --daemonize
./scripts/galaxy-main -c config/galaxy.yml --server-name handler_1 --attach-to-pool job-handlers --attach-to-pool workflow-scheduler --daemonize
./scripts/galaxy-main -c config/galaxy.yml --server-name handler_3 --attach-to-pool job-handlers --attach-to-pool workflow-scheduler --daemonize
./scripts/galaxy-main -c config/galaxy.yml --server-name special_0 --attach-to-pool job-handlers.special --daemonize
```

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

### Access dataset by number with get()

Source: https://github.com/galaxyproject/galaxy/blob/dev/test-data/selenium-test-notebook.ipynb

Opens a dataset from the Galaxy history using its dataset number. The example calls get(1) and returns the file path as a string.

```python
get(1)  # noqa: F821
```

```text
Result:
'/import/1'
```

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

### Install and enable Apache modules on Debian

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/apache.md

Install Apache and enable the required modules (headers, deflate, expires, rewrite, proxy) on Debian-based systems. The output shows the modules being enabled and reminds to restart Apache.

```shell-session
# apt-get install apache2
$ a2enmod headers deflate expires rewrite proxy
Enabling module headers.
Considering dependency filter for deflate:
Module filter already enabled
Module deflate already enabled
Enabling module expires.
Enabling module rewrite.
Enabling module proxy.
To activate the new configuration, you need to run:
  service apache2 restart
```

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

### Conda upgrade conflict error

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/conda_faq.rst

Example error output when the upgrade command fails due to a dependency conflict with the installed Python version. The error indicates that the conda version requires a different Python version than the one installed.

```bash
UnsatisfiableError: The following specifications were found to be in conflict:
  - conda ==4.6.14 -> python >=3.6,<3.7.0a0
  - python 3.5*
Use "conda info <package>" to see the dependencies for each package.
```

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

### Initial Population: python scripts/tool_source/populate_store.py -c

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/tool_source_storage.rst

Performs the initial population of the tool source store using the short -c option for the configuration file.

```console
$ python scripts/tool_source/populate_store.py -c /path/to/galaxy.yml
```

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

### Install pydantic-ai Provider Extras for Anthropic and Google

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/ai_agents.md

Install the required provider extras for `pydantic-ai` to use Anthropic or Google models. Use `pydantic-ai[anthropic]` for `anthropic:` prefixed models and `pydantic-ai[google]` for `google:` prefixed models. Needed when Anthropic or Google models fail with ImportError.

```bash
pip install 'pydantic-ai[anthropic]'   # for anthropic: prefixed models
pip install 'pydantic-ai[google]'       # for google: prefixed models
```

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

### Complete GalaxyUserTool example with matching inputs and outputs

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/agents/prompts/custom_tool_structured.md

Shows a complete GalaxyUserTool definition where every $(inputs.X) in shell_command matches a declared input, and the output's from_work_dir matches the file the command writes. The command uses head -n with an integer input and a quoted file path, writing to output.txt.

```yaml
class: GalaxyUserTool
id: head-lines
name: Head lines
version: 0.1.0
container: quay.io/biocontainers/coreutils:9.5
shell_command: head -n $(inputs.num_lines) '$(inputs.input_file.path)' > output.txt
inputs:
    - name: input_file
      type: data
      label: Input file
    - name: num_lines
      type: integer
      value: 10
      label: Number of lines
outputs:
    - name: output_file
      type: data
      from_work_dir: output.txt
      label: First lines
```

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

### Check Python version

Source: https://github.com/galaxyproject/galaxy/blob/dev/README.rst

Galaxy requires Python 3.10 or higher. Run this command to verify your Python version.

```console
$ python -V
Python 3.10.12
```

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

### Populate tool source store with populate_store.py

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/tool_source_storage.rst

Builds the SQLite file from a writable host. For file-backed SQLite targets, writes a sidecar manifest; failure to write it fails the command. --dry-run and in-process population do not produce manifests.

```console
$ python scripts/tool_source/populate_store.py -c galaxy.yml --target cvmfs_main
```

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

### Create a clean virtualenv for Galaxy

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/production.md

Use a clean Python interpreter to avoid conflicts in $PYTHONPATH or site-packages. This sequence creates a virtualenv without site packages, activates it, and starts Galaxy with run.sh.

```default
nate@weyerbacher% pip install virtualenv
nate@weyerbacher% virtualenv --no-site-packages galaxy_env
nate@weyerbacher% . ./galaxy_env/bin/activate
nate@weyerbacher% cd galaxy-dist
nate@weyerbacher% sh run.sh
```

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

### Keep tests focused and independent

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Shows good and bad examples: the good test checks a single loading state, while the bad test tries to cover multiple concerns.

```typescript
// ✅ Good: Focused test
test("displays loading state", () => {
    const wrapper = mount(MyComponent, {
        props: { loading: true },
    })
    expect(wrapper.find('[role="status"]').exists()).toBe(true)
})

// ❌ Bad: Multiple concerns
test("component does everything", () => {
    // Tests loading, error, success, navigation...
})
```

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

### Basic Usage: python scripts/tool_source/populate_store.py --config

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/tool_source_storage.rst

Populates the tool source store using the Python script. The --config option is required and does not assume a default path. It discovers tools from tool configs, parses each tool with macro expansion, computes a content hash, and stores sources in the configured backend, skipping unchanged tools.

```console
$ python scripts/tool_source/populate_store.py --config /path/to/galaxy.yml
```

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

### Test data factory example

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Use factory functions for consistent test data, such as getFakeRegisteredUser.

```typescript
import { getFakeRegisteredUser } from "@tests/test-data";

const user = getFakeRegisteredUser({ id: "custom-id", is_admin: true });
```

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

### Manual linting setup

Source: https://github.com/galaxyproject/galaxy/blob/dev/packages/README.md

Equivalent to syncing the package environment and adding Galaxy's linting dependencies. Runs ruff check on the galaxy-auth package.

```bash
$ uv sync --locked --package galaxy-auth --all-extras
$ uv pip install -r ../../lib/galaxy/dependencies/pinned-lint-requirements.txt
$ uv run --locked --package galaxy-auth ruff check .
```

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

### Clone Galaxy to shared filesystem

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/cluster.md

Install Galaxy into a directory on a shared filesystem accessible from all cluster nodes. The path must be identical on the application server and nodes.

```console
galaxy_user@galaxy_server% git clone https://github.com/galaxyproject/galaxy.git /clusterfs/galaxy/galaxy-app
```

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

### Type-safe API calls with createGalaxyApi

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/packages/api-client/README.md

Shows how to create the API client and make type-safe GET requests, with responses typed as HistorySummary[] | undefined. Also demonstrates using the HistorySummary type for variables.

```typescript
import { createGalaxyApi, type HistorySummary, type DatasetEntry } from "@galaxyproject/galaxy-api-client";

const api = createGalaxyApi();

// Type-safe API calls
const { data: histories } = await api.GET("/api/histories");
// histories is typed as HistorySummary[] | undefined

// You can use the types for your variables
const myHistory: HistorySummary = {
    id: "123",
    name: "My History",
    // ...other required properties
};
```

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

### Use real queries over test IDs

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Shows good and bad examples: the good test uses accessible queries (aria-label, role) while the bad test uses a test ID.

```typescript
// ✅ Good: Uses accessible queries
const button = wrapper.find('button[aria-label="Submit"]')
const error = wrapper.find('[role="alert"]')

// ❌ Avoid: Test IDs unless necessary
const button = wrapper.find('[data-testid="submit-btn"]')
```

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

### PostgreSQL database URL using a non-standard socket directory

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/production.md

Use this URL when connecting to a PostgreSQL server on the same host and the socket is in a non-standard location, such as the default on Debian/Ubuntu (`/var/run/postgresql`). Adjust the host path as needed for your installation.

```default
postgresql+psycopg:///mydatabase?host=/var/run/postgresql
```

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

### Start tusd server for resumable uploads

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/nginx.md

Run tusd to listen on localhost:1080, store uploads in database/tmp, and send authentication hooks to Galaxy. Replace <galaxy_url> and <galaxy_root> with your actual values.

```sh
tusd -host localhost -port 1080 -upload-dir=<galaxy_root>/database/tmp -hooks-http=<galaxy_url>/api/upload/hooks -hooks-http-forward-headers=X-Api-Key,Cookie
```

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

### Parameterize config with papermill

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy_test/selenium/jupyter/notebook_example_testing.ipynb

Cell tagged with 'parameters' so it can be parameterized with papermill. If config is not overridden, ./galaxy_selenium_context.yml can also be populated.

```python
# Cell is tagged with 'parameters' so it can be parameterized with papermill,
# if config not overridden ./galaxy_selenium_context.yml can also be populated.
config = None
```

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

### Working with Histories using createGalaxyApi

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/packages/api-client/README.md

Configures the API client with a base URL and API key, then lists histories, retrieves the most recently used history, gets history details, and updates a history with a new name and annotation.

```typescript
import { createGalaxyApi } from "@galaxyproject/galaxy-api-client";

const api = createGalaxyApi({
    baseUrl: "https://usegalaxy.org",
    apiKey: "your-api-key",
});

// List all histories
const { data: histories, error } = await api.GET("/api/histories");

// Get most recently used history
const { data: recent } = await api.GET("/api/histories/most_recently_used");

// Get history details
const { data: history } = await api.GET("/api/histories/{history_id}", {
    params: { path: { history_id: "abc123" } },
});

// Update a history
const { data: updated } = await api.PUT("/api/histories/{history_id}", {
    params: { path: { history_id: "abc123" } },
    body: { name: "My Analysis", annotation: "RNA-seq experiment" },
});
```

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

### Tool configuration XML with ToolShed tool

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/tool_panel.rst

Shows a tool panel section with a tool installed from a ToolShed. The `tool_path` attribute sets the base directory for tool files. The `tool` element includes a `guid` attribute and child elements specifying the ToolShed repository details.

```xml
<toolbox tool_path="shed_tools">
    <section id="metagenomics" name="Metagenomics" version="">
        <tool file="toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/2d4c0825cfe6/picrust_predict_metagenomes/predict_metagenomes.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/1.0.1.0">
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>picrust_predict_metagenomes</repository_name>
            <repository_owner>iuc</repository_owner>
            <installed_changeset_revision>2d4c0825cfe6</installed_changeset_revision>
            <id>toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/1.0.1.0</id>
            <version>1.0.1.0</version>
        </tool>
    </section>
</toolbox>
```

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

### Test user-visible behavior vs implementation details

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Shows good and bad test examples: the good test checks user-visible behavior (error message) while the bad test checks implementation details (calling fetchData method).

```typescript
// ✅ Good: Tests user-visible behavior
test("displays error message when API fails", async () => {
    vi.mocked(ToolShedApi).mockReturnValue({ error: { status: 500 } })
    const wrapper = mount(MyComponent)
    await flushPromises()
    expect(wrapper.text()).toContain("Error loading data")
})

// ❌ Bad: Tests implementation details
test("calls fetchData method", () => {
    const fetchDataSpy = vi.spyOn(wrapper.vm, "fetchData")
    // ...
})
```

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

### Create DriverWrapper instance

Source: https://github.com/galaxyproject/galaxy/blob/dev/packages/selenium/README.rst

Parse arguments and create a DriverWrapper instance to adapt them to a NavigatesGalaxy instance.

```python
args = parser.parse_args()
driver_wrapper = cli.DriverWrapper(args)
```

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

### Set per-user Celery task rate limit to 0.1

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/production.md

Configure `celery_user_rate_limit` to a non-zero float to limit tasks per user per second. Example allows at most one task every 10 seconds; default 0.0 disables rate limiting.

```yaml
celery_user_rate_limit: 0.1
```

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

### XML tool command with database and filesystem access

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/user_defined_tools.md

Example of a standard Galaxy XML tool command section that queries the Galaxy database and writes a file to the home directory of the system user running the Galaxy process. This level of access is acceptable only when administrators install tools.

```xml
<command><![CDATA[
    #from pathlib import Path
    #user_id = $__app__.model.session().query($__app__.model.User.id).one()
    #open(f"{Path.home()}/a_file", "w").write("Hello!")
]]></command>
```

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

### Descriptive Test Names

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Use clear and descriptive test names that describe what is being tested. Good examples include 'displays error banner when API returns 500' and 'hides submit button when form is invalid'. Avoid vague names like 'works correctly'.

```typescript
// ✅ Good: Clear and descriptive
test("displays error banner when API returns 500", async () => {})
test("hides submit button when form is invalid", () => {})

// ❌ Bad: Vague
test("works correctly", () => {})
test("component test", () => {})
```

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

### Run commands with uv

Source: https://github.com/galaxyproject/galaxy/blob/dev/packages/tool_shed/CLAUDE.md

Example of running Python and pytest commands using uv from the package directory to ensure the correct environment.

```bash
uv run python -c "from selenium.webdriver.common.by import By; print(By.CLASS_NAME)"
uv run pytest tests/seleniumtests/test_has_driver.py -v
```

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

### LocalVue setup with getLocalVue helper

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Use the shared getLocalVue() helper to configure BootstrapVue, Pinia, localization, and common directives. Optionally pass true for localization instrumentation to test l() calls.

```typescript
const localVue = getLocalVue();
// or with localization instrumentation for testing l() calls:
const localVue = getLocalVue(true);
```

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

### Vue Template Spacing: Between Non-Connected Elements

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of adding space between non-connected elements. The 'Do' example includes a blank line between the spans; the 'Don't' example omits it.

```vue
<div>
    <span>
        First span.
    </span>

    <span>
        Second span.
    </span>
</div>
```

```vue
<div>
    <span>
        First span.
    </span>
    <span>
        Second span.
    </span>
</div>
```

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

### Lint and format client code with make client-lint and make client-format

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Run these commands before submitting a pull request to ensure code is properly formatted according to Prettier.

```bash
make client-lint
```

```bash
make client-format
```

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

### Install tox with pip

Source: https://github.com/galaxyproject/galaxy/blob/dev/test/TESTING.md

Install tox in your Python virtualenv before running Galaxy tests.

```bash
pip install tox
```

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

### Initialize Galaxy Selenium context with init(config)

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy_test/selenium/jupyter/notebook_example_library.ipynb

Imports the init function from galaxy.selenium.jupyter_context and creates a Galaxy Selenium context using the config variable defined in the previous cell.

```python
from galaxy.selenium.jupyter_context import init

gx_selenium_context = init(config)
```

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

### Configure ready_window_size in job_conf.xml

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/jobs.md

Equivalent XML setting using the ready_window_size attribute on the <handlers> element. Place existing handler definitions inside the element.

```xml
<handlers ready_window_size="100">
    <!-- Existing handler definitions go here. -->
</handlers>
```

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

### Run client dev server with make

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/README.md

Starts the client development server on port 5173 with automatic rebuild and reload. Open http://localhost:5173 instead of the default 8080.

```bash
make client-dev-server
```

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

### Vue Template Spacing: Between Conditional Elements

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of NOT adding space between elements connected by conditionals (v-if/v-else). The 'Do' example has no blank line between the spans; the 'Don't' example incorrectly adds one.

```vue
<div>
    <span v-if="conditional">
        condition met
    </span>
    <span v-else>
        condition not met
    </span>
</div>
```

```vue
<div>
    <span v-if="conditional">
        condition met
    </span>

    <span v-else>
        condition not met
    </span>
</div>
```

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

### Local or shared-filesystem destination with containerized metadata

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/containerized_metadata.md

Configure a local or shared-filesystem cluster destination in job_conf.yml to run metadata with a container. Replace the example release with the version matching your server; prefer the registry's image@sha256:<digest> reference once validated. The engine must be available on the execution host. For Singularity, use engine: singularity, enable singularity_enabled on the destination, and provide an image reference supported by your configured container resolver. Keep the explicit-container resolver enabled and avoid destination-wide tool-image overrides such as container_override or docker_container_id_override, as they take precedence over the explicit metadata image.

```yaml
runners:
  local:
    load: galaxy.jobs.runners.local:LocalJobRunner
execution:
  default: metadata_docker
  environments:
    metadata_docker:
      runner: local
      docker_enabled: true
      outputs_to_working_directory: true
      metadata_strategy: extended
      metadata_config:
        containerize: true
        engine: docker
        image: quay.io/galaxyproject/galaxy-job-execution:26.1.1
```

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

### NGINX proxy_cache_path for Tool Shed install info

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/doc/nginx_caching.md

Declares a cache zone named toolshed_install_info in the http block. Adjust paths and sizes as needed; the zone stores cached responses for the install info routes.

```nginx
proxy_cache_path /var/cache/nginx/toolshed
                 levels=1:2
                 keys_zone=toolshed_install_info:10m
                 max_size=1g
                 inactive=24h
                 use_temp_path=off;
```

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

### Install samtools 0.1.19 with Conda for Galaxy

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/conda_faq.rst

Manually install a Conda dependency for Galaxy. The environment name must follow the pattern `__<package>@<version>` and the package is installed from the bioconda channel. Galaxy will find this environment when tools require samtools version 0.1.19.

```bash
$ conda create --name __samtools@0.1.19 samtools==0.1.19 --channel bioconda

```

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

### Rapid Local Dev with Bootstrapped Data

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Runs the backend with environment overrides for a bootstrap admin API key, HG for dev, and a custom Vite port (4040) for faster local development.

```shell
TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey \
TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 \
TOOL_SHED_VITE_PORT=4040 \
./run_tool_shed.sh
```

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

### ShedTestCase example: repository creation test

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/test/base/README.md

Shows how to subclass ShedTestCase and use create_category, get_or_create_repository, and upload_file to set up a repository test.

```python
class TestFeature(ShedTestCase):
    def test_repo_creation(self):
        category = self.create_category(name="Tools")
        repo = self.get_or_create_repository(
            name="mytool",
            category=category,
            strings_displayed=["created"],
        )
        self.upload_file(repo, "mytool.tar")
```

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

### Build a custom tool panel from scratch (YAML)

Source: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/tool_panel.rst

Defines a completely new tool panel without referencing original sections. It includes a label, a tool, and a custom section with a tool.

```yaml
name: Custom Panel Filter
type: generic
items:
- type: label
  text: The Start
- type: tool
  id: empty_list
- type: section
  id: my-section
  name: My Custom Section
  items:
  - type: tool
    id: count_list
```

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

### Vue Component Spacing: Between script, template, style

Source: https://github.com/galaxyproject/galaxy/blob/dev/client/docs/styleguide.md

Shows the recommended practice of adding empty lines between the `<script>`, `<template>`, and `<style>` blocks in a Vue component. The 'Do' example includes the blank lines; the 'Don't' example omits them.

```vue
<script setup>
// do stuff...
</script>

<template>
    <!--template stuff-->
</template>

<style lang="scss" scoped>
// style stuff...
</style>
```

```vue
<script setup>
// do stuff...
</script>
<template>
    <!--template stuff-->
</template>
<style lang="scss" scoped>
// style stuff...
</style>
```

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

### Test Composition API components with mount()

Source: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/webapp/frontend/CLAUDE.md

Shows how to test a Composition API component by mounting it and interacting with it as a user would (clicking a button).

```typescript
import { mount } from "@vue/test-utils"
import { describe, it, expect, vi, beforeEach } from "vitest"
import MyComponent from "@/components/MyComponent.vue"

describe("MyComponent", () => {
    it("updates count when button clicked", async () => {
        const wrapper = mount(MyComponent)
        const button = wrapper.find("button")
        await button.trigger("click")
        expect(wrapper.text()).toContain("Count: 1")
    })
})
```
Tokens:
Raw