PipelineDog-CLI

A command line interface for PipelineDog.

Installation

• First, make sure you have Node.js installed on your machine. To check,

  node -v

  You should see a version number.

  If not, you need to install Node.js first.

  • Install using Linuxbrew

    • Install Linuxbrew

    ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)"

    • Install node

    brew install node

  • Installing using Binary (without sudo access)

    • For example, download Linux binary x64 platform in home folder. You should download the binary that suits your platform:

    cd ~
    wget https://nodejs.org/dist/v6.11.3/node-v6.11.3-linux-x64.tar.xz

    • Unzip the package:

    tar -xz node-v6.11.3-linux-x64.tar.xz

    • Add executables to PATH:

    PATH=$PATH:/home/node-v6.11.3-linux-x64/bin

For certain Linux distribution (e.g., Ubuntu 14.04), a legacy version of npm is installed under the name "nodejs", not "node". For these systems, a current version of (v6 or later) should be installed.

For installing node through packager manager and additional information on installing Node.js, please refer to the Nodejs installation guide.

• Once Node.js is installed, install the PipelineDog CLI:

  npm install -g pipelinedog

• After doing this, you'll be able to see the help information by typing:

  pipelinedog -h

  in the terminal.

Usage:

• Use

  pipelinedog -h

  to invoke the manual:

  Usage: pipelinedog [options]
  
  Options:
  
    -h, --help            output usage information
    -v, --version         output the version number
    -p, --project <path>  your PipelineDog project file
    -l, --list <path>     file lists for the run, separated by commas
    -o, --output [path]   path to output shell command file

• For a comprehensive documentation and explanation of concepts, please visit the PipelineDog Wiki

Example:

• An example for running commandline PipelineDog:

  • Copy the content of the example PipelineDog project at http://pipeline.dog/gatk.yml and save it as a local file named gatk.yml, or download the file using:

  wget http://pipeline.dog/gatk.yml

  • Copy the content of the example list file at http://pipeline.dog/Default_List and save it as a local file named Default_List, or download the file using:

  wget http://pipeline.dog/Default_List

  • In the same folder, run

  pipelinedog -p gatk.yml -l Default_List -o cmd.sh

  • The command output will be saved in cmd.sh. It can be later executed in a Linux environment with appropiate tools installed. To view the content of cmd.sh, run

  cat cmd.sh