PipelineDog-CLI
A command line interface for PipelineDog.
Installation
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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.
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Once Node.js is installed, install the PipelineDog CLI:
npm install -g pipelinedog
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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
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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