gxtk

Usage

usage: gxtk [-h]
            {find,reload,requirements,env-name,conda-commands,mulled-hash,delete-histories,test,get-tools,decode,show-keys}
            ...

Sub-commands:

find

Filter tool list for a galaxy instance by properties including repository name, display name and owner. Default output is a tab separated table of tools. Optional return fields include bio.tools ID. Admin users can include the tool’s conda environment name (-e flag) in output.

gxtk find [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
          [--profiles_path PROFILES_PATH] [-n NAME] [-N DISPLAY_NAME]
          [-v VERSION] [-o OWNER [OWNER ...]] [-z]
          [-t TOOL_IDS [TOOL_IDS ...]] [-V] [-s SECTION_LABEL] [--all_tools]
          [--labels LABELS [LABELS ...]]
          [--biotools [BIOTOOLS [BIOTOOLS ...]]]
          [--edam_topics [EDAM_TOPICS [EDAM_TOPICS ...]]] [-e]
          [-f OUTPUT_FORMAT] [-S SOURCE]

Named Arguments

-g, --galaxy_url

URL of Galaxy instance

-a, --api_key

Galaxy api key

-p, --profile

Key for profile set in profiles yaml file

--profiles_path

Path to profiles yaml file (default ~/.gxtk.yml)

-n, --name

Tool repository name

-N, --display_name

User facing tool name

-v, --version

Version

-o, --owner

Show tools from one or more owners

-z, --fuzz

Match substring of repository name from search term

Default: False

-t, --tool_ids

One or more tool ids to match exactly

-V, --all_versions

Search from complete list of tools including older versions

Default: False

-s, --section_label

Tool Section label

--all_tools

Show all installed tools

Default: False

--labels

Tool label

--biotools

Enter flag to show bio.tools IDs in output, add arguments to filter by bio.tool IDs

Default: [‘DO_NOT_DISPLAY’]

--edam_topics

Enter flag to show Edam topics in output, add arguments to filter by topics

Default: [‘DO_NOT_DISPLAY’]

-e, --env

Show virtual environment name (admin API key required)

Default: False

-f, --output-format

Format of output list plain(default)|tsv

Default: “plain”

-S, --source

Path to a json file containing tool list

reload

Reload tool in panel

gxtk reload [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
            [--profiles_path PROFILES_PATH] -t TOOL_ID

Named Arguments

-g, --galaxy_url: URL of Galaxy instance
-a, --api_key: Galaxy api key
-p, --profile: Key for profile set in profiles yaml file
--profiles_path: Path to profiles yaml file (default ~/.gxtk.yml)
-t, --tool_id: Tool ID

requirements

Print conda package requirements for tool ID (admin only).

gxtk requirements [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
                  [--profiles_path PROFILES_PATH] -t TOOL_ID

Named Arguments

-g, --galaxy_url: URL of Galaxy instance
-a, --api_key: Galaxy api key
-p, --profile: Key for profile set in profiles yaml file
--profiles_path: Path to profiles yaml file (default ~/.gxtk.yml)
-t, --tool_id: Tool ID

env-name

Print conda environment name for tool ID (admin only).

gxtk env-name [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
              [--profiles_path PROFILES_PATH] -t TOOL_ID

Named Arguments

-g, --galaxy_url: URL of Galaxy instance
-a, --api_key: Galaxy api key
-p, --profile: Key for profile set in profiles yaml file
--profiles_path: Path to profiles yaml file (default ~/.gxtk.yml)
-t, --tool_id: Tool ID

conda-commands

Print out conda command for uninstalling and reinstalling an environment from <conda dir>/envs directory where the conda base enviroment is active. The purpose is for reinstalling environments where the environment has errors.

gxtk conda-commands [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
                    [--profiles_path PROFILES_PATH] -t TOOL_ID [-m]

Named Arguments

-g, --galaxy_url

URL of Galaxy instance

-a, --api_key

Galaxy api key

-p, --profile

Key for profile set in profiles yaml file

--profiles_path

Path to profiles yaml file (default ~/.gxtk.yml)

-t, --tool_id

Tool ID

-m, --mamba

Use mamba instead of conda in install command

Default: False

mulled-hash

Generate a galaxy conda mulled hash (v1) from a list of requirements

gxtk mulled-hash [-h] requirements [requirements ...]

Positional Arguments

requirements: One or more conda requirements e.g. balloon=1.1 or fish=3.2b

delete-histories

Delete histories belonging to user. This will wait for small histories that can be deleted within 2-3 minutes. For histories that take longer than nginx takes to time out, the script waits until the history has state ‘deleted’ unless the –skip_wait flag is included in the command.

gxtk delete-histories [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
                      [--profiles_path PROFILES_PATH]
                      [--name_startswith NAME_STARTSWITH]
                      [--days_since_updated DAYS_SINCE_UPDATED] [--delete_all]
                      [--skip_wait] [-y] [--user_email USER_EMAIL]

Named Arguments

-g, --galaxy_url

URL of Galaxy instance

-a, --api_key

Galaxy api key

-p, --profile

Key for profile set in profiles yaml file

--profiles_path

Path to profiles yaml file (default ~/.gxtk.yml)

--name_startswith

History name prefix

--days_since_updated

Last updated more than X days ago

--delete_all

In the absence of conditions include this argument to delete all histories

Default: False

--skip_wait

Do not wait while large histories are deleted, allow them to delete in the background

Default: False

-y, --yes

Skip confirmation step prior to deleting histories

Default: False

--user_email

Email address of user account. This provides an optional extra integrity check that the API key provided was for the intended user

test

Wrapper for galaxy-tool-util’s galaxy-tool-test.

gxtk test [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
          [--profiles_path PROFILES_PATH] -t TOOL_ID [--tags TAGS [TAGS ...]]
          [--results_dir RESULTS_DIR] [--test_data TEST_DATA [TEST_DATA ...]]
          [-P PARALLEL_TESTS]

Named Arguments

-g, --galaxy_url

URL of Galaxy instance

-a, --api_key

Galaxy api key

-p, --profile

Key for profile set in profiles yaml file

--profiles_path

Path to profiles yaml file (default ~/.gxtk.yml)

-t, --tool_id

Tool ID

--tags

Tags for test history

--results_dir

base directory for tool test results (defaults to $GXTK_RESULTS_DIR)

--test_data

Local test data paths

-P, --parallel_tests

Number of tests to run in parallel

Default: 1

get-tools

Save tool list to a JSON or yaml file.

gxtk get-tools [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
               [--profiles_path PROFILES_PATH] [-o OUTPUT_PATH] [-f FORMAT]

Named Arguments

-g, --galaxy_url

URL of Galaxy instance

-a, --api_key

Galaxy api key

-p, --profile

Key for profile set in profiles yaml file

--profiles_path

Path to profiles yaml file (default ~/.gxtk.yml)

-o, --output_path

Output file name

-f, --format

Format (yaml or json, default json)

Default: “json”

decode

Translate API ID to integer database ID (admin only).

gxtk decode [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
            [--profiles_path PROFILES_PATH]
            api_id

Positional Arguments

api_id: Encoded hexadecimal object ID

Named Arguments

-g, --galaxy_url: URL of Galaxy instance
-a, --api_key: Galaxy api key
-p, --profile: Key for profile set in profiles yaml file
--profiles_path: Path to profiles yaml file (default ~/.gxtk.yml)

show-keys

List keys in profiles file (~/.gxtk.yml by default)

gxtk show-keys [-h] [-g GALAXY_URL] [-a API_KEY] [-p PROFILE]
               [--profiles_path PROFILES_PATH]

Named Arguments

-g, --galaxy_url: URL of Galaxy instance
-a, --api_key: Galaxy api key
-p, --profile: Key for profile set in profiles yaml file
--profiles_path: Path to profiles yaml file (default ~/.gxtk.yml)