v0.1.7

1) bug fix for deepcopy,  2) basename for URL includes hash of URL (t…

v0.1.6

• Bug fix for URL (due to typo if -> elif)

v0.1.5

• auth error handling for cURL (added curl_auto_auth())

v0.1.4

• replace subprocess.run() with subprocess.Popen() for old python3 (<3.5)
• change RE pattern to capture cURL error

v0.1.3

• bug fix
  • caper_uri: typo in URL -> S3 transfer command
• URL to cloud transfer is two-step
  • URL to local and then local to cloud (gcs, s3)
• use call-caching by default
• can use both _ and - in a configuration file
• added -m to specify metadata JSON file destination
• fix Java heap memory for run (1G) and server (2G)

v0.1.2.3

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)

v0.1.2

Cromweller changed its name to caper.

v0.1.1

• added shell scripts to /mysql/ to start a MySQL server with Docker or Singularity.
• supports soft linking for local-to-local file transfer.
• explicitly show symlinking instead of copying if it makes a symlink.
• for run mode, build singularity image before running a pipeline (local backend only).
  • fix for multiple tasks trying to build on the same image when there is no pre-built image.

v0.1.0

First beta release