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cromshell-draft-release-2.0.0
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مشاهده بیشترتوضیحات
Command Line Interface (CLI) for Cromwell servers
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cromshell-draft-release-2.0.0 |
| نام | cromshell-draft-release |
| نسخه کتابخانه | 2.0.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Jonn Smith, Louis Bergelson, Beri Shifaw |
| ایمیل نویسنده | jonn@broadinstitute.org, louisb@broadinstitute.org, bshifaw@broadinstitute.org |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/cromshell-draft-release/ |
| مجوز | BSD 3-Clause |
```
__ __
.,-;-;-,. /'_\ +-----------------------------------------------+ /_'\.,-;-;-,.
_/_/_/_|_\_\) / | CROMSHELL : run Cromwell jobs from the shell | \ (/_/__|_\_\_
'-<_><_><_><_>=/\ +-----------------------------------------------+ /\=<_><_><_><_>-'
`/_/====/_/-'\_\ /_/'-\_\====\_\'
"" "" "" "" "" ""
```
# Cromshell
[](https://badge.fury.io/gh/broadinstitute%2Fcromshell)
[](https://github.com/broadinstitute/cromshell/actions/workflows/integration_tests.yml/badge.svg)
[](https://github.com/broadinstitute/cromshell/actions/workflows/unit_tests.yml/badge.svg)
[](https://opensource.org/licenses/MIT)
Cromshell is a CLI for submitting workflows to a Cromwell server and monitoring/querying their results.
## Examples:
```
cromshell submit workflow.wdl inputs.json options.json dependencies.zip
cromshell status
cromshell -t 20 metadata
cromshell logs -2
```
## Supported Options:
* `--no_turtle` or `--I_hate_turtles`
* Hide turtle logo
* `--cromwell_url [TEXT]`
* Specifies Cromwell URL used.
* `TEXT` Example: `http://65.61.654.8:8000`
* Note: Depending on your Cromwell server configuration, you may not need to specify the port.
* `-t [TIMEOUT]`
* Specifies the server connection timeout in seconds.
* Default is 5 sec.
* `TIMEOUT` must be a positive integer.
* `--gcloud_token_email [TEXT]`
* Call `gcloud auth print-access-token` with
this email and add the token as an auth header to requests.
* `--referer_header_url [TEXT]`
* For servers that require a referer, supply
this URL in the `Referer:` header.
## Supported Subcommands:
#### Start/Stop workflows
* `submit [-w] <wdl> <inputs_json> [options_json] [included_wdl_zip_file]`
* Automatically validates the WDL and JSON file.
* Submit a new workflow to the Cromwell server.
* *`-w`* [COMING SOON] Wait for workflow to transition from 'Submitted' to some other status before ${SCRIPTNAME} exits.
* *`included_wdl_zip_file`* Zip file containing any WDL files included in the input WDL
* `abort [workflow-id] [[workflow-id]...]`
* Abort a running workflow.
#### Workflow information:
* `alias <workflow-id> <alias_name>`
* Label the given workflow ID with the given alias_name. Aliases can be used in place of workflow IDs to reference jobs.
* Remove an alias by passing empty double quotes as `alias_name` (e.g. `alias <workflow-id> ""`)
#### Query workflow status:
* `status [workflow-id] [[workflow-id]...]`
* Check the status of a workflow.
* `metadata [workflow-id] [[workflow-id]...]`
* Get the full metadata of a workflow.
* `slim-metadata [workflow-id] [[workflow-id]...]`
* Get a subset of the metadata from a workflow.
* `counts [-j] [-x] [workflow-id] [[workflow-id]...]`
* Get the summarized status of all jobs in the workflow.
* `-j` prints a JSON instead of a pretty summary of the execution status (compresses subworkflows)
* `-x` compress sub-workflows for less detailed summarization
* `timing` *`[workflow-id] [[workflow-id]...]`*
* Open the timing diagram in a browser.
#### Logs
* `logs [workflow-id] [[workflow-id]...]`
* List the log files produced by a workflow.
* [COMING SOON] `fetch-logs [workflow-id] [[workflow-id]...]`
* Download all logs produced by a workflow.
#### Job Outputs
* `list-outputs [workflow-id] [[workflow-id]...]`
* List all output files produced by a workflow.
* [COMING SOON] `fetch-all [workflow-id] [[workflow-id]...]`
* Download all output files produced by a workflow.
#### Display a list jobs submitted through cromshell
* `list [-c] [-u]`
* `-c` Color the output by completion status.
* `-u` Check completion status of all unfinished jobs.
#### Clean up local cached list
* [COMING SOON] `cleanup [-s STATUS]`
* Remove completed jobs from local list.
This command removes all jobs from the local list that are in a completed state,
where a completed state is one of: `Succeeded`, `Failed`, `Aborted`
* *`-s [STATUS]`* If provided, will only remove jobs with the given `[STATUS]` from the local list.
#### Update cromwell server
* `update-server`
* Change the cromwell server that new jobs will be submitted to.
#### Get cost for a workflow
* `cost [-c] [-d] [workflow-id] [[workflow-id]...]`
* Get the cost for a workflow.
* Only works for workflows that completed more than 24 hours ago on GCS. See [Google Cost Exporting Documentation](https://cloud.google.com/billing/docs/how-to/export-data-bigquery-tables)
* Billing export to BigQuery must be enabled for your GCP billing project.
See [Setup billing data export to BigQuery](https://cloud.google.com/billing/docs/how-to/export-data-bigquery-setup).
* Requires the `bq_cost_table` key to exist in the cromshell
configuration file and have a value equal to the BigQuery cost table
for your GCP billing project.
* `-c/--color` Color outliers in task level cost results.
* `-d/--detailed` Get the cost for a workflow at the task level.
## Features:
* Running `submit` will create a new folder in the `~/.cromshell/${CROMWELL_URL}/` directory named with the cromwell job id of the newly submitted job.
It will copy your wdl and json inputs into the folder for reproducibility.
* It keeps track of your most recently submitted jobs by storing their ids in `./cromshell/`
You may omit the job ID of the last job submitted when running commands, or use negative numbers to reference previous jobs, e.g. "-1" will track the last job, "-2" will track the one before that, and so on.
* You can override the default cromwell server by setting the argument `--cromwell_url` to the appropriate URL.
* You can override the default cromshell configuration folder by setting the environmental variable `CROMSHELL_CONFIG` to the appropriate directory.
* Most commands takes multiple workflow-ids, which you *can specify both in relative and absolute ID value* (i.e. `cromshell status -- -1 -2 -3 c2db2989-2e09-4f2c-8a7f-c3733ae5ba7b`).
* Assign aliases to workflow ids using the alias command (i.e. `cromshell alias -- -1 myAliasName`).
Once the Alias command is used to attach an alias to a workflow id, the alias name can be used instead of the id (i.e. `cromshell status myAliasName`).
## Installation
From brew
brew tap broadinstitute/dsp
brew install cromshell@2.0.0.beta.1
From pypi
pip install -i https://test.pypi.org/simple/ cromshell-draft-release
From source
git clone git@github.com:broadinstitute/cromshell.git
cd cromshell
pip install .
cromshell --help
## Uninstallation
From brew
brew uninstall cromshell@2.0.0.beta.1
From pypi/source
pip uninstall cromshell
## Development
See the [Developer Docs](./developer_docs/)
## Legacy Cromshell
The original Cromshell shell script is still available in the legacy_cromshell folder and in the `cromshell1` branch of this repository.
It is no longer maintained, but is still available for use. The original Cromshell contains some commands not yet available in Cromshell2,
such as `fetch-logs`, `fetch-all`, `notify`, and `cleanup`. These commands will be added to Cromshell2 in the future.
نیازمندی
| مقدار | نام |
|---|---|
| >=2022.3.0 | gcsfs |
| >=3.5.0 | google-cloud-bigquery |
| >=1.1.0 | termcolor |
| >=8.0.0 | click |
| >=2.27.1 | requests |
| >=2.12.0 | pygments |
| >=0.8.9 | tabulate |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl cromshell-draft-release-2.0.0:
pip install cromshell-draft-release-2.0.0.whl
نصب پکیج tar.gz cromshell-draft-release-2.0.0:
pip install cromshell-draft-release-2.0.0.tar.gz