Contents

# GENOMER-INIT 1

## NAME

genomer-init(1) -- create a new genomer project

## SYNOPSIS

`genomer init` *project-name*

## DESCRIPTION

Creates a new genomer project directory named **project-name**. Returns an
error if the project directory already exists. This created directory has the
following structure. Each file is described below.

    **project-name**
    ├── Gemfile
    └── assembly
        ├── annotations.gff
        ├── scaffold.yml
        └── sequence.fna

* **Gemfile**: Genomer plugins are specified here. After adding a plugin the
  command `bundle install` should run to install the required plugins. Gems are
  specified according to [the bundler documentation][bundler]. Each plugin
  should begin with the suffix 'genomer-plugin.'

* **sequence.fna**: The file containing your contigs and scaffolds. These
  should be stored in fasta format.

* **scaffold.yml**: The specifies the final layout of your genome. The scaffold
  file is written the YAML format. Details and examples of the scaffold format
  can be found on the [next.gs][] website.

* **annotations.gff**: Specific your genome annotations in [gff3 format][gff]
  here. The **seqid** column should match the corresponding name of the fasta
  sequence in the **sequence.fna** file.

[bundler]: http://gembundler.com/
[gff]: http://www.sequenceontology.org/gff3.shtml
[next.gs]: http://next.gs

## BUGS

**Genomer-init** is written in Ruby and uses several RubyGems dependencies. See
the Gemfile in the genomer gem install directory for version details.

## COPYRIGHT

**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

Version data entries

4 entries across 4 versions & 1 rubygems

Version	Path
genomer-0.1.0	man/genomer-init.1.ronn
genomer-0.0.10	man/genomer-init.1.ronn
genomer-0.0.9	man/genomer-init.1.ronn
genomer-0.0.8	man/genomer-init.1.ronn