antha/elements repository overview

⁠Antha Elements

This repo is for storing and running Antha protocols.

⁠Installation

Main instructions are in antha-lang/antha⁠.

⁠Update submodels

git submodule update --init

⁠Build

To build or update elements in the elements folder:

make
# or
make current

or run this command from anywhere:

make -C "$(go list -f '{{.Dir}}' github.com/antha-lang/elements)"

By default, make will download and update any dependent libraries. If you have any modifications to these dependencies (e.g., non-master branches), make current will build elements without updating any dependent libraries.

If your elements are stored elsewhere you can change the target directory to comile with make by adding AN_DIRS=<your-directory-here> e.g...

make -C $HOME/go/src/github.com/antha-lang/elements AN_DIRS=$HOME/Documents

⁠Setting up anthabuild as an alias

The tutorial material will refer to using anthabuild as a command to recompile all antha elements. You can set up the anthabuild alias by running this command:

⁠On Mac

cat<<EOF>>$HOME/.bash_profile
alias anthabuild='make -C "$(go list -f '{{.Dir}}' github.com/antha-lang/elements)"'
EOF
source ~/.bash_profile

⁠On Linux

cat<<EOF>>$HOME/.bashrc
alias anthabuild='make -C "$(go list -f '{{.Dir}}' github.com/antha-lang/elements)"'
EOF
source ~/.bashrc

Important: this will build elements stored in the elements folder, if your elements are stored elsewhere the anthabuild command should be appended with AN_DIRS= when running or initially setting up the anthabuild alias.

e.g.

anthabuild AN_DIRS=$GOPATH/src/github.com/my-antha-elements

⁠Test

To run tests ok all example workflows:

make test

⁠Run

antha run --bundle workflow-and-parameters.json

⁠Help

antha --help

⁠Academy

Go to the Antha Academy⁠ page to be guided through how to use antha in more detail.