Skip to content

v0.1.2.3

Choose a tag to compare

View all tags
@leepc12 leepc12 released this 19 May 10:19
v0.1.2.3
8ae2f1a
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

Caper can be PIP-installed.

$ pip install caper

Three executables will be installed. caper, run_mysql_server_singularity.sh and run_mysql_server_docker.sh.

$ caper
/home/ec2-user/miniconda3/lib/python3.7/site-packages/caper/caper.py
usage: caper [-h] [-c FILE] {run,server,submit,abort,unhold,list,metadata} ...

positional arguments:
  {run,server,submit,abort,unhold,list,metadata}
    run                 Run a single workflow without server
    server              Run a Cromwell server
    submit              Submit a workflow to a Cromwell server
    abort               Abort running/pending workflows on a Cromwell server
    unhold              Release hold of workflows on a Cromwell server
    list                List running/pending workflows on a Cromwell server
    metadata            Retrieve metadata JSON for workflows from a Cromwell
                        server

optional arguments:
  -h, --help            show this help message and exit
  -c FILE, --conf FILE  Specify config file
(base) [ec2-user@ip-172-30-0-159 ~]$ run_mysql_server_
run_mysql_server_docker.sh       run_mysql_server_singularity.sh

$ run_mysql_server_docker.sh
Usage: ./run_mysql_server_docker.sh [DB_DIR] [PORT] [MYSQL_USER] [MYSQL_PASSWORD] [CONTAINER_NAME]

Example: run_mysql_server_docker.sh ~/cromwell_data_dir 3307

[DB_DIR]: This directory will be mapped to '/var/lib/mysql' inside a container
[PORT] (optional): MySQL database port for docker host (default: 3306)
[MYSQL_USER] (optional): MySQL username (default: cromwell)
[MYSQL_PASSWORD] (optional): MySQL password (default: cromwell)
[CONTAINER_NAME] (optional): MySQL container name (default: mysql_cromwell)

$ run_mysql_server_singularity.sh
Usage: ./run_mysql_server_singularity.sh [DB_DIR] [PORT] [MYSQL_USER] [MYSQL_PASSWORD] [CONTAINER_NAME]

Example: run_mysql_server_singularity.sh ~/cromwell_data_dir 3307

[DB_DIR]: This directory will be mapped to '/var/lib/mysql' inside a container
[PORT] (optional): MySQL database port for singularity host (default: 3306)
[MYSQL_USER] (optional): MySQL username (default: cromwell)
[MYSQL_PASSWORD] (optional): MySQL password (default: cromwell)
[CONTAINER_NAME] (optional): MySQL container name (default: mysql_cromwell)
Assets 2
Loading