Pipelinedog NPM

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
```