INSTALLING COMPTER ------------------ Dependencies ------------ Perl ---- Compter is written in Perl so you'll need to have a perl installation to run it. There's almost certainly one on any unix system you want to run this on already, but you can check by opening a shell and running: perl -V If you don't have perl then you can install it through your system's package managed (yum, apt-get etc) Perl Modules ------------ Compter uses one non-core Perl module, which is the Cwd module. You can install this with: perl -MCPAN -e 'install Cwd' ..if it's not installed already. R language ---------- For the heatmap compter uses R to do the clustering and drawing. You will therefore need a valid R installation to be able to use the full functionality of the program (you can run it using --nograph if you don't have R but you won't get the pretty picture). R is available from http://cran.r-project.org R packages ---------- Compter uses the pheatmap package in R to draw the heatmap. You will need to install this to get the program to work. To install pheatmap and any dependencies it requires simply open an R session and run: install.packages("pheatmap") Installing compter ------------------ Until there is an official release of compter we recommend installing by doing a checkout of the latest development version: git clone https://github.com/s-andrews/compter.git You will then need to either add the compter install directory into your path, or symlink (DON'T COPY) the compter program into a directory already in your path. Running the test data --------------------- To check that compter is installed correctly and working, move into the "test" directory in the compter install and run: compter -background mouse -o test.txt high_seqs.fa low_seqs.fa You should see output like: Reading background from /bi/apps/compter/backgrounds/mouse.cmp Processing high_seqs.fa ... Processing low_seqs.fa .. Drawing heatmap ..and you should create output files: test.txt and test.png Problems, Bugs etc ------------------ If you have any problems with the program please report them in the issue tracker on the github project page. If you have any questions then please send them to simon.andrews@babraham.ac.uk