Readme for 1.0.0

README.md

@@ -3,31 +3,30 @@ ARIBA
 
 Antibiotic Resistance Identification By Assembly
 
-For how to use ARIBA, please see the [ARIBA wiki page] [ARIBA wiki].
+For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
 
 
 
 Installation
 ------------
 
 ARIBA has the following dependencies, which need to be installed:
-  * [python3] [Python3] version >= 3.4
-  * [r] [R] version >= 2.14.0
-  * [ape] [ape] version >= 3.1
-  * [bowtie2] [Bowtie2] version >= 2.1.0
-  * [cd-hit] [cdhit] version >= 4.6
-  * [samtools and bcftools] [samtools]  version >= 1.2
-  * [MUMmer] [mummer] version >= 3.23
-  * Either [SPAdes] [spades] version >= 3.5.0 or [Velvet] [velvet] version >= 1.2.07
-    (SPAdes is recommended)
-  * [python2] [Python2] version >= 2.7 (if SPAdes is used, Python2 is also required)
+  * [Python3][python] version >= 3.4
+  * [R][r] version >= 2.14.0
+  * The R package [ape][ape] version >= 3.1
+  * [Bowtie2][bowtie2] version >= 2.1.0
+  * [CD-HIT][cdhit] version >= 4.6
+  * [Samtools and BCFtools][samtools]  version >= 1.2
+  * [MUMmer][mummer] version >= 3.23
+  * [SPAdes][spades] version >= 3.5.0
+  * [Python2][python] version >= 2.7 (SPAdes needs python2)
 
 
 ARIBA has the following optional dependencies. If they are installed,
 they will be used. Otherwise scaffolding and gap filling will be
 skipped.
-  * [SSPACE-basic scaffolder] [sspace]
-  * [GapFiller] [gapfiller]
+  * [SSPACE-basic scaffolder][sspace]
+  * [GapFiller][gapfiller]
 
 Once the dependencies are installed, install ARIBA using pip:
 
@@ -43,10 +42,45 @@ If the tests all pass, install:
     python3 setup.py install
 
 
+### Dependencies and environment variables
+
+By default, ARIBA will look for the dependencies in your `$PATH`, using
+the names in the table below. This behaviour can be overridden and
+point ARIBA to a specific program using environment variables.
+The environment variable is checked first and is used if it is set.
+Otherwise ARIBA looks in your `$PATH` for the default name. This applies
+to the following dependencies.
+
+| Dependency     |  Default               | Environment variable name |
+|----------------|------------------------|---------------------------|
+| BCFtools       | `bcftools`             | `$ARIBA_BCFTOOLS`         |
+| Bowtie2        | `bowtie2`              | `$ARIBA_BOWTIE2`          |
+| CD-HIT         | `cd-hit-est`           | `$ARIBA_CDHIT`            |
+| GapFiller      | `GapFiller.pl`         | `$ARIBA_GAPFILLER`        |
+| R              | `Rscript`              | `$ARIBA_R`                |
+| Samtools       | `samtools`             | `$ARIBA_SAMTOOLS`         |
+| SPAdes         | `spades.py`            | `$ARIBA_SPADES`           |
+| SSPACE         | `SSPACE_Basic_v2.0.pl` | `$ARIBA_SSPACE`           |
+
+
+For example, you could specify an exact version of Samtools using
+(assuming BASH):
+
+    export ARIBA_SAMTOOLS=/path/to/samtools
+
+The path need not be absolute. ARIBA looks for the value of the variable
+in your $PATH. For example, suppose you have `samtools-0.1.19` and
+`samtools-1.3` installed. You could use this:
+
+    export ARIBA_SAMTOOLS=samtools-1.3
+
+
+
+
 Usage
 -----
 
-Please read the [ARIBA wiki page] [ARIBA wiki] for usage instructions.
+Please read the [ARIBA wiki page][ARIBA wiki] for usage instructions.
 
 
 
@@ -61,9 +95,8 @@ Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/ariba.svg?
   [samtools]: http://www.htslib.org/
   [spades]: http://bioinf.spbau.ru/spades
   [sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
-  [velvet]: http://www.ebi.ac.uk/~zerbino/velvet/
   [ape]: https://cran.r-project.org/web/packages/ape/index.html
   [r]: https://www.r-project.org/
-  [python3]: https://www.python.org/
+  [python]: https://www.python.org/
 
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='ariba',
-    version='0.6.0',
+    version='1.0.0',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},