Merge pull request #144 from andrewjpage/master

Manually merge Aidan Delaneys pull request

INSTALL.md

@@ -146,6 +146,7 @@ If you do not have permission to install the software as root and instead want t
 $ wget https://bootstrap.pypa.io/ez_setup.py -O - | python - --user
 $ ~/.local/bin/easy_install -U --user biopython
 $ ~/.local/bin/easy_install -U --user dendropy
+$ autoreconf -i
 $ ./configure --prefix=~/.local
 $ make
 $ make install

install-userspace.sh

@@ -13,7 +13,7 @@
 #
 
 py_pkgs=( "biopython" "dendropy" )
-deb_urls=( "http://uk.archive.ubuntu.com/ubuntu/pool/universe/r/raxml/raxml_7.2.8-2_amd64.deb" "https://launchpad.net/~ap13/+archive/ubuntu/gubbins/+files/fastml2_2.3~trusty1_amd64.deb" "https://launchpad.net/~ap13/+archive/ubuntu/gubbins/+files/gubbins_1.1.1~trusty1_amd64.deb" )
+deb_urls=( "http://uk.archive.ubuntu.com/ubuntu/pool/universe/r/raxml/raxml_7.2.8-2_amd64.deb" "https://launchpad.net/~ap13/+archive/ubuntu/gubbins/+files/fastml2_2.3~trusty1_amd64.deb" "https://launchpad.net/~ap13/+archive/ubuntu/gubbins/+files/gubbins_1.3.3~trusty1_amd64.deb" )
 
 function check_platform {
     # Ubuntu 14.04