BioBB TEMPLATE Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Template_container

Short description for the template container module in Restructured Text (reST) syntax. Mandatory.

Get help

Command:

template_container -h

usage: template_container [-h] [--config CONFIG] --input_file_path1 INPUT_FILE_PATH1 [--input_file_path2 INPUT_FILE_PATH2] --output_file_path OUTPUT_FILE_PATH

Description for the template container module.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_file_path2 INPUT_FILE_PATH2
                        Description for the second input file path (optional). Accepted formats: dcd.

required arguments:
  --input_file_path1 INPUT_FILE_PATH1
                        Description for the first input file path. Accepted formats: top.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_file_path1 (string): Description for the first input file path. File type: input. Sample file. Accepted formats: TOP

  • input_file_path2 (string): Description for the second input file path (optional). File type: input. Sample file. Accepted formats: DCD

  • output_file_path (string): Description for the output file path. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • boolean_property (boolean): (True) Example of boolean property..

  • binary_path (string): (zip) Example of executable binary property..

  • remove_tmp (boolean): (True) Remove temporal files..

  • restart (boolean): (False) Do not execute if output files exist..

  • container_path (string): (None) Container path definition..

  • container_image (string): (mmbirb/zip:latest) Container image definition..

  • container_volume_path (string): (/tmp) Container volume path definition..

  • container_working_dir (string): (None) Container working directory definition..

  • container_user_id (string): (None) Container user_id definition..

  • container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  boolean_property: false
  container_image: mmbirb/zip:latest
  container_path: docker
  container_volume_path: /tmp
  remove_tmp: true

Command line

template_container --config config_template_container.yml --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample

JSON

Common config file

{
  "properties": {
    "boolean_property": false,
    "remove_tmp": true,
    "container_path": "docker",
    "container_image": "mmbirb/zip:latest",
    "container_volume_path": "/tmp"
  }
}

Command line

template_container --config config_template_container.json --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample

Template

Short description for the template module in Restructured Text (reST) syntax. Mandatory.

Get help

Command:

template -h

usage: template [-h] [--config CONFIG] --input_file_path1 INPUT_FILE_PATH1 [--input_file_path2 INPUT_FILE_PATH2] --output_file_path OUTPUT_FILE_PATH

Description for the template module.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_file_path2 INPUT_FILE_PATH2
                        Description for the second input file path (optional). Accepted formats: dcd.

required arguments:
  --input_file_path1 INPUT_FILE_PATH1
                        Description for the first input file path. Accepted formats: top.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_file_path1 (string): Description for the first input file path. File type: input. Sample file. Accepted formats: TOP

  • input_file_path2 (string): Description for the second input file path (optional). File type: input. Sample file. Accepted formats: DCD

  • output_file_path (string): Description for the output file path. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • boolean_property (boolean): (True) Example of boolean property..

  • binary_path (string): (zip) Example of executable binary property..

  • remove_tmp (boolean): (True) Remove temporal files..

  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  boolean_property: false
  remove_tmp: true

Singularity config file

properties:
  boolean_property: false
  container_image: bioexcel-zip_container-master-latest.simg
  container_path: singularity
  container_volume_path: /tmp
  binary_path: /opt/conda/bin/zip
  remove_tmp: false

Command line

template --config config_template.yml --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample

JSON

Common config file

{
  "properties": {
    "boolean_property": false,
    "remove_tmp": true
  }
}

Singularity config file

{
  "properties": {
    "boolean_property": false,
    "remove_tmp": false,
    "binary_path": "/opt/conda/bin/zip",
    "container_path": "singularity",
    "container_image": "bioexcel-zip_container-master-latest.simg",
    "container_volume_path": "/tmp"
  }
}

Command line

template --config config_template.json --input_file_path1 urlto.sample --input_file_path2 urlto.sample --output_file_path urlto.sample