cromshell
CLI for interacting with Cromwell servers
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Download Latest Version (.zip)- integration_tests.yml
- pypi_packaging.yml
- unit_tests.yml
- bq_cost_table.png
- addcommand.md
- addtests.md
- mockdata.md
- publish_release.md
- README.md
- runtests.md
- _cromshell
- reload.sh
- cromshell
- README.md
- no_call_cache.json
- options.json
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command.py
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- command.py
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- command.py
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- command.py
- __init__.py
- command.py
- __init__.py
- command.py
- __init__.py
- command_setup_utils.py
- config_options_file_utils.py
- cromshellconfig.py
- http_utils.py
- io_utils.py
- miniwdl_utils.py
- submissions_file_utils.py
- womtool_utils.py
- workflow_id_utils.py
- workflow_status_utils.py
- __init__.py
- command.py
- __init__.py
- __main__.py
- log.py
- __init__.py
- __init__.py
- test_placeholder.py
- all.workflow.database.tsv
- __init__.py
- conftest.py
- test_abort.py
- test_alias.py
- test_counts.py
- test_list_outputs.py
- test_logs.py
- test_submit.py
- test_update_server.py
- test_validate.py
- test_version.py
- utility_test_functions.py
- GetZmwCounts.metadata.json
- succeeded_helloworld.metadata.json
- cromwell_application.conf
- README.md
- invalid.json
- valid.json
- test_workflow_status_failed_helloword_metadata.txt
- test_workflow_status_succeded_workflow_slim_metadata.txt
- cromwell_output_api_example.json
- helloworld_dict_of_outputs.json
- helloworld_task_level_outputs.txt
- helloworld_workflow_level_outputs.txt
- print_file_like_value_in_dict_example.txt
- print_file_like_value_in_dict_no_indent_example.txt
- succeeded_helloworld.outputs.metadata.json
- fail_Mutect2.json
- local_helloworld_metadata.json
- PAPIV2_helloworld_metadata.json
- success.json
- will_fail.json
- submission_file_template.text
- all.workflow.database.tsv
- cromshell_config.json
- doom_workflow_slim_metadata.json
- failed_helloworld_metadata.json
- failed_workflow_slim_metadata.json
- running_helloworld_metadata.json
- running_workflow_slim_metadata.json
- submitted_helloworld_metadata.json
- succeeded_helloworld_metadata.json
- succeeded_workflow_slim_metadata.json
- __init__.py
- conftest.py
- test_alias.py
- test_config_options_file_utils.py
- test_cost.py
- test_counts.py
- test_cromshellconfig.py
- test_http_utils.py
- test_io_utils.py
- test_list_outputs.py
- test_logs.py
- test_metadata.py
- test_miniwdl_utils.py
- test_slim_metadata.py
- test_status.py
- test_submissions_file_utils.py
- test_submit.py
- test_version.py
- test_workflow_id_utils.py
- hello_world_task.wdl
- helloWorld_with_imports.wdl
- fail-mutect2.inputs.json
- fail-mutect2.wdl
- gpu_cuda_test.json
- gpu_cuda_test.wdl
- helloWorld.json
- helloWorld.wdl
- helloWorldFail.wdl
- mutect2.inputs.json
- mutect2.wdl
- not_valid.json
- not_valid.wdl
- will_fail.json
- will_fail.wdl
- __init__.py
- conftest.py
- .bumpversion.cfg
- .coveragerc
- .gitignore
- .isort.cfg
- .pylintrc
- .readthedocs.yml
- dev-requirements.txt
- LICENSE
- MANIFEST.in
- pyproject.toml
- README.md
- requirements.txt
- test-requirements.txt
- tox.ini
# Installation Guide
1. Get the code
git clone https://github.com/broadinstitute/cromshell
Downloads the entire project code from GitHub to your computer.
cd cromshell
Moves into the project folder you just downloaded.
2. Official Install Script
Easy Recommendedbrew tap broadinstitute/dsp
Registers this project's repository (tap) with Homebrew.
brew install cromshell
Installs the pre-built package via Homebrew โ no source build required.
pip install cromshell
Installs the package published on PyPI directly โ no need to clone the source.
pip install .
Installs the package published on PyPI directly โ no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Python
EasyPrerequisites
pip install cromshell
Installs the package published on PyPI directly โ no need to clone the source.
pip install .
Installs the package published on PyPI directly โ no need to clone the source.
pip uninstall cromshell
Type this command into your terminal and run it.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
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