https://github.com/broadinstitute/cromshell - 2.1.1

Version Bump (#275)

- Python
Published by bshifaw over 2 years ago

https://github.com/broadinstitute/cromshell - 2.1.0

Additions

• PR265 Added validate command: When invoked performs WDL workflow validation using Cromwell's womtool API and miniwdl. It checks the syntax and type errors in the provided WDL and its associated input JSON file, and it can also optionally handle local imports via miniwdl. If successful, it prints "Validation successful"; otherwise, it prints "Validation failed."
• PR268 Flatten and submit nested WDLs: This update addresses a common issue regarding path resolution in nested directory structures when working with WDLs. It introduces a new feature to the submit command, which automatically detects relative imports in workflows, creates a temporary directory, and rewrites WDLs with adjusted imports, making it easier to work with dependencies both within and outside of Terra. ## Bug Fixes
• PR256 Fix to have the version command print the version
• PR271 Fix to have metadata and slim-metadata print machine-readable json

- Python
Published by bshifaw over 2 years ago

https://github.com/broadinstitute/cromshell - 2.0.0

We are excited to announce the release of Cromshell 2! This new version of Cromshell brings a number of improvements and new features to the Cromwell job submission experience.

Here are some of the key highlights of Cromshell 2: - A completely rebuilt codebase in Python, which brings improved reliability, performance, and modularity to the tool. - Automatic zipping of workflow dependencies when submitting a workflow. - Integration and unit tests to ensure Cromshell remains a reliable and robust tool. - Multiple installation options: Cromshell 2 can be installed from source, via Homebrew, or from PyPI. - A modular architecture that makes adding new functionalities and commands easier. - Developer documentation that provides guidance on how to add new features and commands to the tool.

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shell script is still available in the legacy_cromshell folder and in the cromshell1 branch of this repository.It is no longer maintained, but is still available for use.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.

- Python
Published by bshifaw about 3 years ago

https://github.com/broadinstitute/cromshell - 2.0.0.beta.1

Beta release of Cromshell2

Added commands:

• alias - Label the given workflow ID with the given alias
• counts - Get the summarized status of all jobs in the workflow (same as execution-status-count)
• list - Display a list of jobs submitted through cromshell
• logs - List the log files produced by a workflow.
• timing - Open the timing diagram in a browser.
• update-server - Change the Cromwell server to which new jobs will be submitted.

Added features - Developer documentation - Step-by-step instructions on adding new commands and their tests to cromshell. #195 - Automatically zip dependency files when submitting a workflow. #214 - Support for users running Cromshell against Cromwell server in Terra workspace. Contributed by the Cromwell team. #208

- Python
Published by bshifaw over 3 years ago

https://github.com/broadinstitute/cromshell - 0.5.3

Bug fix release. ad30776 Fixes cost and detailed cost queries for new billing setup as of 2022 Aug 11 (#219) e119c23 Add note about cromshell 2 alpha to readme (#211) bb9a1b1 Fixing issue where tasks would be incorrectly labeled as failed. (#190)

- Python
Published by lbergelson over 3 years ago

https://github.com/broadinstitute/cromshell - 2-alpha.1

Alpha release of Cromshell2

This is a rewrite in python which is currently not feature complete with the original. You can view it and contribute in the cromshell_2.0 branch.

Contains the following commands: - abort - Abort a running workflow. - metadata - Get the full metadata of a workflow. - slim-metadata - Get a subset of the workflow metadata. - status - Check the status of a Cromwell job UUID - submit - Submit a workflow and arguments to the Cromwell Server

Please see the Please see the README for python installation instructions.

- Python
Published by bshifaw over 4 years ago

https://github.com/broadinstitute/cromshell - 0.5.2

You can now add header parameters to your curl requests using the new CROMSHELL_HEADER environment variable. This is useful for cromwell servers that add an authentication layer based on oath headers.

c619d26 Update README.md (#178) f0f8033 Add curl headers (#175) cbcb0e8 Add note about bq init to README (#170)

- Python
Published by lbergelson over 4 years ago

https://github.com/broadinstitute/cromshell -

Bugfixes! d047632 Fix timing command #167 (#168) c6389c5 Updating wait time for cost and cost-detailed from 8h to 24h (#166)

- Python
Published by lbergelson almost 5 years ago

https://github.com/broadinstitute/cromshell - 0.5.0

New Feature: Workflow costs.

• New commands cost and cost-detailed which lookup the cost of completed workflows and show the total or per-task costs. These require a new config file ~/.cromshell/gcp_bq_cost_table.config which includes the name of your google cloud costs BigQuery table.
  

4df19a6 Readme and completions fixups (#165) 90a5f53 Adding zsh completions for cost commands (#164) 3e0586f Added cost commands. (#163) 69d2e4a Removing another temporary file from notify daemon. (#162)

- Python
Published by lbergelson almost 5 years ago

https://github.com/broadinstitute/cromshell -

Added a new update-server command to rerun the server initialization dialog.

4787986 Add the sub-command "update-server" (#140) c2e8c7b explicitly prepend http to server address when IP address is used instead of an url (#145) c7ea883 Fixing issue with aliases and GNU grep. (#136)

- Python
Published by lbergelson almost 5 years ago

https://github.com/broadinstitute/cromshell -

A minor release with the following changes:

bea7396 Adding server name to submit command output. (#134) #133 006e8e7 Excluded the notify daemon from the jq version check. (#128)

- Python
Published by lbergelson almost 6 years ago

https://github.com/broadinstitute/cromshell -

Minor new features and bug fixes:

4f53689 Enable alias matching for non-standard form commands (#122) d6db1ae Add counts as shorter alias of execution-status-count (#123) 2074728 highlight failed shards in execution-status-count (#125) 06c3373 disallow dash and whitespace in alias names (#121) 4407626 update list function to handle permanently offline servers (#119)

- Python
Published by lbergelson about 6 years ago

https://github.com/broadinstitute/cromshell -

Bug Fixes, even more attempts to fix subworkflow expansion.

d144f0b more fixes for subworkflows #112 (#116) 81faa4e Fixing cleanup command. (#117) c982d2b Fix execution-status-count -x -p (#114)

- Python
Published by lbergelson over 6 years ago

https://github.com/broadinstitute/cromshell -

New features:

• Workflow Aliases: You can now assign aliases to workflows using the new alias command and then reference them by alias instead of workflow id.

• Zsh tab completion: There is a new fully featured zsh completion script for zsh in /completions.

Complete Change List: 1773860 Add zsh completion script (#111) 1f22848 Update jq query to understand subworkflows (#107) 27948ce Fix false positive doom. (#106) e31cfd1 Adding in functionality for aliasing jobs. (#104) 283ae00 Improve on the name WILL_FAIL (#103)

- Python
Published by lbergelson over 6 years ago

https://github.com/broadinstitute/cromshell -

Release with two small improvements:

a39d3c9 allow custom slim-metadata parameters e402a22 Suppressing extraneous files from the list-outputs command. (#102)

- Python
Published by lbergelson over 6 years ago

https://github.com/broadinstitute/cromshell -

New Feature: Notify is now aware of the WILL_FAIL status and will report at the time it first detects a failure rather than waiting for workflow completion.

968f2ed Fixed notification daemon for different local/remote cromwell servers. (#96) caec4d3 Added WILL_FAIL as a terminal state for the notify daemon. (#91) f848a38 Update to README.md

- Python
Published by lbergelson over 6 years ago

https://github.com/broadinstitute/cromshell -

New feature: when submitting a workflow, if womtool is in your path it will be used to validate the wdl and json before uploading.

Womtool can be installed with brew install cromwell

bc1ff8b Fixing small bug with nested subworkflows (#88) f2d394c Added womtool validation for WDL/JSON if it's in your path. (#87)

- Python
Published by lbergelson almost 7 years ago

https://github.com/broadinstitute/cromshell -

New Feature: cromshell status and list now check if any of the jobs in a running workflow have failed and will report a new WILL_FAIL status.

1282fe0 Various cleanup refactoring (#86) a400bd5 Added in a WILL_FAIL status for workflows that will fail. (#85) 7d466ea Now directly queries the cromwell instance to prove it exists. (#83)

- Python
Published by lbergelson almost 7 years ago

https://github.com/broadinstitute/cromshell -

Fix submitting with dependencies (#82)

- Python
Published by lbergelson almost 7 years ago

https://github.com/broadinstitute/cromshell -

fix a bug introduced in 0.3.5 69ae84c Fixed error in execution-status-count with relative IDs. (#80)

- Python
Published by lbergelson about 7 years ago

https://github.com/broadinstitute/cromshell -

New Feature: execution-status-count -p argument to pretty pretty print results.

e190f40 Tidy up code in cleanup function (#77) e1fa14d Check that files exist and are non-empty before submitting(#76) 81b4a21 Fixed regression of relative job ID failure. (#74) e65f1e2 Update README.md (#72) f649e1a Pretty execution-status-count implementation (#67)

- Python
Published by lbergelson about 7 years ago

https://github.com/broadinstitute/cromshell -

A small release with improvements to execution-status-count so it works with larger arrays of jobs. Also two bug fixes.

48c7755 Improve turtle shell pattern stability under moving conditions (#69) 47b5314 Increase performance of execution-status-count (#65) 79824e1 Fixed issue with list-outputs. (#64)

- Python
Published by lbergelson about 7 years ago

https://github.com/broadinstitute/cromshell -

Minor fixes: 416f9b5 printing subcommand to sdterr instead of stdout (#61) 69d18ba Added in protections to kill the turtleSpinner on exit. (#59) ec2fafd red dead turtle (#57)

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell -

A bug fix release. This fixes a bug that broke cromshell notify (#55) which was introduced in 0.3.0

4230e2e Fixed issue with notify daemon. (#56)

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell -

Small release which adds a new global -t argument to configure the curl timeout.

044d549 Curl timeouts (#54)

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell -

This version removes the default cromwell url and adds a setup process for first time users. Set up can be skipped by providing a ~/.cromshell/cromwellserver.config file or setting the `CROMWELLURL` environment variable.

The previous default was: https://cromwell-v36.dsde-methods.broadinstitute.org

New features: * submit -w flag to wait until the job has started or failed with (appropriate waiting animation) * initial configuration so no default server is assumed * cleanup command to remove old runs

d615309 Added in -w flag for submit command. (#50) bd2ac67 preventing error message when invoking cromshell with no args (#52) 17aed47 Added in basic first-time run config. (#47) 4123ab1 Update readme to reflect new behavior for workflow ids (#48) ed41a26 Added a cleanup command to cromshell. (#46) e8e1316 Refactored to use getopts in some places. (#45)

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell -

Status turtle is more dramatic on failure.

2db1018 Dramatic dead turtle (#44) c74e81c add note to readme about bioconda (#40)

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell - 0.2.3

Changes: * moved the turtle to stderr instead of stdout * expand subworkflows when getting metadata

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell -

Minor release, a bug fix and the addition of a turtle. a084fe0 fix ping url (#34) - Thank you @huangzhibo aa3e47d turtle status (#31)

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell -

Bug fix release: * fixes a crash on systems which default to python3

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell - 0.2.0 release

Changes and new features!

New commands, new features, new storage locations!

New commands

• fetch-logs: download all of the logs for a workflow
• list-outputs: list the outputs created by a workflow
• fetch-all: download logs AND outputs for a workflow... potentially VERY large....
• list: display a list of all the jobs submitted through cromshell

New Features

• id directories are now stored in the ~/.cromshell directory in a subdirectory corresponding to which cromwell server ran them
• cromshell now keeps track of which server a job ran on will connect to the correct one on subsequent connections
• updated the default server to methods cromwell 36
• better cromshell --help output, improved readme

- Python
Published by lbergelson over 7 years ago

https://github.com/broadinstitute/cromshell - First cromshell release!

This is the first labelled release of cromshell.

It includes some big changes from previous version.
1. The cromwell script has been renamed to cromshell. This allows both cromshell and the actual cromwell tools to be installed together and not conflict. 2. There's a new notify command which allows you to receive email when your job is complete. Very useful! 3. The script has been totally refactored to support better error messages and status codes.

- Python
Published by lbergelson over 7 years ago