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Init man contains details of the created project

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30 man/genomer-init.1.ronn
@@ -11,7 +11,35 @@ genomer-init(1) -- create a new genomer project
## DESCRIPTION
Creates a new genomer project directory named **project-name**. Returns an
-error if the project directory already exists.
+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

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