https://github.com/otiai10/uge_cooker

Univa Grid Engine Recipe Cooker
https://github.com/otiai10/uge_cooker

bioinformatics gridengine hpc

Last synced: 16 days ago
JSON representation

Univa Grid Engine Recipe Cooker

• Host: GitHub
• URL: https://github.com/otiai10/uge_cooker
• Owner: otiai10
• Created: 2017-04-28T01:57:58.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-08-28T02:36:42.000Z (over 7 years ago)
• Last Synced: 2024-10-30T03:49:22.422Z (2 months ago)
• Topics: bioinformatics, gridengine, hpc
• Language: Python
• Homepage:
• Size: 20.5 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# uge_cooker

Univa Grid Engine Recipe Cooker

# Why?

- bad to handle envs and options in script files

	- good to separate operations and project-specific things

- bad to execute duplicate commands to follow logs

	- good to just hit the same command for each project to follow logs

- bad to specify job names only to deal `-hold_jid`

	- good to autommatically generate `-hold_jid`

# Installation

```sh

$ pip install git+https://github.com/otiai10/uge_cooker.git

$ which uge_cooker

```

```sh

# Try it first!!

$ git clone https://github.com/otiai10/uge_cooker.git

$ cd uge_cooker/example_project

$ uge_cooker -r recipe.json

```

# Example

```json

{

  "jobs": [

    {

      "name": "hello_01",

      "script": "./hello_01.sh",

      "options": {}

    },

    {

      "name": "hello_02",

      "script": "./hello_02.sh",

      "options": {

        "-hold_jid": "$$PREVIOUS_JOB_ID"

      }

    }

  ]

}

```

then

```sh

$ uge_cooker --recipe your_recipe.json

```

# Basic Usage

```sh

uge_cooker -r recipe.json -E env.json

```

# Tail mode

to follow tails of logs in current directory (where recipe.json is placed)

```sh

uge_cooker -t .

```

# Options

| option | value | description |

|:-------:|:-------:|:-----------:|

| -t,--tail | **required, if provided** | Execute `tail -f logs/**/*/*` to follow logs,
would abort any options else |

| -r,--recipe | **required, if provided** | Recipe json file path, which specifies operation details,
 must be `.json` |

| -E,--env    | optional default ` ` | Specify env json file path, which specifies env vars,
 must be `.json` if provided |

| -v,--verbose | optional, no value | Turn on verbose logs of what commands are exactly executed |

| -S,--slack | optional | Comma separated usernames of you Slack team (1) |

1. To use `--slack` option, you need export 2 env vars `COOKER_SLACK_TOKEN` and `COOKER_SLACK_CHANNEL` to your environment, on which you execute `uge_cooker` command.