[med-svn] [snp-sites] 01/07: Imported Upstream version 2.3.2

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository snp-sites.

commit 7553b47bce873eec4714da721df91f9009cb2150
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon May 16 10:35:04 2016 +0000

    Imported Upstream version 2.3.2
---
 README.md  | 5 ++++-
 VERSION    | 2 +-
 src/main.c | 4 ++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 5928c9f..6d36cdd 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@ Rapidly decreasing genome sequencing costs have led to a proportionate increase
 
 The software can be cited as:
 
-[Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", bioRxiv, doi: http://dx.doi.org/10.1101/038190 (2016).](http://biorxiv.org/content/early/2016/01/29/038190)
+["SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)](http://dx.doi.org/10.1099/mgen.0.000056)
 
 ```
 Usage: snp-sites [-mvph] [-o output_filename] <file>
@@ -70,6 +70,7 @@ There are a few ways to install snp-sites. The simpliest way is using apt (Debia
 * OSX - using HomeBrew
 * OSX/Linux - from source
 * OSX/Linux - from a release tarball
+* Windows/OSX/Linux - using a Virtual Machine
 
 ## Linux - Ubuntu/Debian
 If you have a recent version of Ubuntu or Debian then you can install it using apt.
@@ -124,3 +125,5 @@ make
 sudo make install
 ```
 
+## Windows/OSX/Linux - using a Virtual Machine
+A virtual machine (VM) is available containing the software. More details can be found on [the Pathogen VM page](http://sanger-pathogens.github.io/pathogens-vm/).
diff --git a/VERSION b/VERSION
index 2bf1c1c..f90b1af 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.3.1
+2.3.2
diff --git a/src/main.c b/src/main.c
index 299c7d5..2740817 100644
--- a/src/main.c
+++ b/src/main.c
@@ -50,8 +50,8 @@ static void print_usage()
 
   printf("If you use this program, please cite:\n");
   printf("\"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments\",\n");
-  printf("Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016),\n");
-  printf("bioRxiv doi: http://dx.doi.org/10.1101/038190\n");
+  printf("Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris,\n");
+  printf("Microbial Genomics 2(4), (2016). http://dx.doi.org/10.1099/mgen.0.000056\n");
   
 }
 

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