Merge pull request #149 from andrewjpage/mafft

Mafft and exonerate dependancies
sanger-pathogens · Jun 12, 2015 · c291f57 · c291f57
2 parents 51d73a9 + 5bfae6a
commit c291f57
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diff --git a/README.md b/README.md
@@ -23,7 +23,7 @@ Roary takes annotated assemblies as input in GFF3 format, such as those produced
 Assuming you have root on your system, all the dependancies can be installed using apt and cpanm (only tested on Ubuntu 14.04).
 
 ```
-sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank
+sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft exonerate
 sudo cpanm -f Bio::Roary
 ```   
 
@@ -38,7 +38,7 @@ Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.s
 
 ```
 brew tap homebrew/science
-brew install bedtools cd-hit blast mcl parallel prank
+brew install bedtools cd-hit blast mcl parallel prank mafft exonerate
 cpanm -f Bio::Roary
 ```
 

diff --git a/install_dependencies.sh b/install_dependencies.sh
@@ -37,7 +37,9 @@ sudo apt-get install -y -q g++ \
                            libdb-dev \
                            libssl-dev \
                            ncbi-blast+ \
-                           mcl
+                           mcl \
+                           exonerate \
+                           mafft 
 
 download () {
   download_url=$1