Merge pull request #6 from martinghunt/master

Move usage info to wiki

README.md

@@ -3,11 +3,14 @@ ARIBA
 
 Antibiotic Resistance Identification By Assembly
 
+For how to use ARIBA, please see the [ARIBA wiki page] [ARIBA wiki].
+
+
 
 Installation
 ------------
 
-Dependencies:
+ARIBA has the following dependencies, which need to be installed:
   * [samtools and bcftools] [samtools]  version >= 1.2
   * [SSPACE-basic scaffolder] [sspace]
   * [GapFiller] [gapfiller]
@@ -16,7 +19,7 @@ Dependencies:
   * Either [SPAdes] [spades] version >= 3.5.0 or [Velvet] [velvet] version >= 1.2.07
     (SPAdes is recommended)
 
-Install with pip:
+Once the dependencies are installed, install ARIBA using pip:
 
     pip3 install pyfastaq
 
@@ -30,30 +33,19 @@ If the tests all pass, install:
     python3 setup.py install
 
 
-
 Usage
 -----
 
-The installation will put a single script called `ariba` in your path.
-The usage is:
-
-    ariba <command> [options] <required arguments>
-
-Run just `ariba` to get a list of tasks. Use `-h` or `--help`
-with a task to get the help, for example
-
-    ariba run --help
-
-To run the pipeline to identify the genes present in a pair of FASTQ files:
-
-    ariba run reference_genes.fa reads_1.fastq reads_2.fastq Output_directory
-
+Please read the [ARIBA wiki page] [ARIBA wiki] for usage instructions.
 
 
+  [ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki
   [gapfiller]: http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller
   [mummer]: http://mummer.sourceforge.net/
   [samtools]: http://www.htslib.org/
   [smalt]: https://www.sanger.ac.uk/resources/software/smalt/
   [spades]: http://bioinf.spbau.ru/spades
   [sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
   [velvet]: http://www.ebi.ac.uk/~zerbino/velvet/
+
+