github.com/antha-lang/antha/component


License
GPL-2.0
Install
go get github.com/antha-lang/antha/component

Documentation

antha

GoDoc Build Status

Antha v0.0.2

Installation Instructions

OSX

First step is to install or upgrade to go 1.5. Follow the instructions at the Golang site.

After you install go, if you don't have Homebrew, please install it. Then, follow these steps to setup a working antha development environment:

# Setup environment variables
cat<<EOF>>$HOME/.bash_profile
export GOPATH=$HOME/go
export PATH=\$PATH:$HOME/go/bin
EOF

# Reload your profile
. $HOME/.bash_profile

# Install the xcode developer tools
xcode-select --install

# Install some external dependencies
brew update
brew install homebrew/science/glpk sqlite3

# Install antha
go get github.com/antha-lang/antha/cmd/...

Linux

Depending on your Linux distribution, you may not have the most recent version of go available from your distribution's package repository. We recommend you download go directly.

For Debian-based distributions like Ubuntu on x86_64 machines, the installation instructions follow. If you do not use a Debian based system or if you are not using an x86_64 machine, you will have to modify these instructions by replacing the go binary with one that corresponds to your platform and replacing apt-get with your package manager.

# Install go
curl -O https://storage.googleapis.com/golang/go1.5.3.linux-amd64.tar.gz
sudo tar -C /usr/local -xzf go1.5.3.linux-amd64.tar.gz

# Setup environment variables
cat<<EOF>>$HOME/.bash_profile
export GOPATH=$HOME/go
export PATH=\$PATH:/usr/local/go/bin:$HOME/go/bin
EOF

# Reload your profile
. $HOME/.bash_profile

# Install antha external dependencies
sudo apt-get install -y libglpk-dev libsqlite3-dev git

# Now, we are ready to get antha
go get github.com/antha-lang/antha/cmd/...

Windows

Installing antha on Windows is significantly more involved than for OSX or Linux. The basic steps are:

  • Setup a go development environment:
    • Install the source code manager git
    • Install go
    • Install the compiler mingw. Depending on whether you installed the 386 (32-bit) or amd64 (64-bit) version of go, you need to install the corresponding version of mingw.
  • Download antha external dependencies
    • Install glpk development library and make sure that mingw can find it.

If this procedure sounds daunting, you can try using some scripts we developed to automate the installation procedure on Windows. Download, unzip them and run install.bat. This will try to automatically apply the Windows installation procedure with the default options. Caveat emptor.

Checking Your Installation

After following the installation instructions for your machine. You can check if Antha is working properly by running a test protocol

cd $GOPATH/src/github.com/antha-lang/antha/antha/examples/workflows/constructassembly
antharun --workflow workflow.json --parameters parameters.yml

Making and Running Antha Components

The easiest way to start developing your own antha components is to place them in the antha/component/an directory and follow the structure of the existing components there. Afterwards, you can compile and use your components with the following commands:

cd $GOPATH/src/github.com/antha-lang/antha
make
go get github.com/antha-lang/antha/cmd/...
antharun --workflow myworkflowdefinition.json --parameters myparameters.yml

Demo

asciicast