Hi,
Thanks for trying out Roary. Hopefully we'll get it sorted quickly.

What operating system and version are you using? The easiest way to install the dependancies is to use homebrew (osx), linuxbrew (linux) or apt (ubuntu). If your installing the dependancies manually, its a bit of a pain I'm afraid, which is why I recommend using the methods just mentioned, although I do appreciate that its not possible for everyone.

In the mcl download, the mcxdeblast script is in ./src/alien/oxygen/src/mcxdeblast
After you have done ' ./configure && make ' you need to add xxxx/src/alien/oxygen/src to your PATH.
FastTree also appears to be missing. The (install_dependancies.sh)[https://github.com/sanger-pathogens/Roary/blob/master/install_dependencies.sh] script builds all the dependancies from source (so that it will work on TravisCI, which is Ubuntu 12.04), which might help if you are comfortable with reading BASH scripts.

Andrew

Dear Andrew,

Thanks, your help solved my problem.
I needed to /src/alien/oxygen/src to my path (and also installed FastTree), and roary runs smoothly.

The reason that i did not use brew is that I got the following error and therefore found it easier to pursue a strategy installing dependencies myself:
rlmn@node1:>brew install mcl
==> Installing mcl from homebrew/homebrew-science
Error: homebrew/science/mcl cannot be built with any available compilers.
To install this formula, you may need to:
brew install gcc
rlmn@node1:>brew install gcc
==> Installing dependencies for gcc: zlib, xz, gmp, mpfr, libmpc, isl
==> Installing gcc dependency: zlib
Error: zlib cannot be built with any available compilers.
To install this formula, you may need to:
brew install gcc
rlmn@node1:>brew install zlib
Error: zlib cannot be built with any available compilers.
To install this formula, you may need to:
brew install gcc

Best of regards from a research camp in Uruguay. Sitting here with greetings from Gregorio Bentancor who motivated to try out Roary.

Rasmus.

Hi Rasmus,
Great to hear you got it working, and it seems to be a very small world indeed!

That error with brew and gcc it a funny chicken and egg problem! To solve it you install gcc with your own packaging system (most likely there already) and then link it so that brew can use it. So if you had version 4.8 of gcc you would do:

ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.8
ln -s $(which g++) ~/.linuxbrew/bin/g++-4.8
ln -s $(which gfortran) ~/.linuxbrew/bin/gfortran-4.8

where '.linuxbrew' is the directory where you installed linuxbrew. Then brew should work.

Andrew

Quick note for others who run across this: If you are installing mcl on your own you can add the --enable-blast option to the configure script to get the mcxdeblast exectuable. See the mcl homebrew formula for an example.

Thanks for the tip