ALLMAPS: How to install

Please use the following if the quick installation method does not work for you.

1. Install Biopython

$ wget http://biopython.org/DIST/biopython-1.63.tar.gz
$ tar -zxvf biopython-1.63.tar.gz
$ cd biopython-1.63
$ python setup.py build
$ python setup.py test
$ python setup.py install --user

2. Install numpy

$ wget http://sourceforge.net/projects/numpy/files/NumPy/1.8.1/numpy-1.8.1.tar.gz
$ tar -zxvf numpy-1.8.1.tar.gz 
$ python setup.py build
$ python setup.py install --user

3. Install DEAP

$ wget https://pypi.python.org/packages/source/d/deap/deap-1.0.1.tar.gz
$ tar -zxvf deap-1.0.1.tar.gz
$ cd deap-1.0.1
$ python setup.py install --user

4. Install NetworkX

$ wget https://pypi.python.org/packages/source/n/networkx/networkx-1.8.1.tar.gz
$ tar -zxvf networkx-1.8.1.tar.gz
$ cd networkx-1.8.1/
$ python setup.py build
$ python setup.py install --user

5. Install matplotlib

$ wget https://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.3.1/matplotlib-1.3.1.tar.gz
$ tar -zxvf matplotlib-1.3.1.tar.gz
$ cd matplotlib-1.3.1
$ python setup.py build
$ python setup.py install --user

6. Install JCVI dependencies: concorde, faSize and liftOver

6.1 From github

$ git clone git://github.com/tanghaibao/jcvi-bin.git
$ cp jcvi-bin/bin/* ~/bin            # ~/bin is your own PATH

6.2 Recompile

If you cannot execute the binaries, recompile manually.

# Recompile concorde 
$ wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
$ unzip jksrc.zip
$ cd kent
$ uname -m                          # check your MACHTYPE
$ export MACHTYPE=i686              # for example, your MACHTYPE is i686    
$ mkdir ~/bin/$MACHTYPE             # Kent apps will go to this directory
$ cd src                            
$ make                              
$ ls -all ~/bin/$MACHTYPE           # check do you have faSize and liftOver
$ export PATH=~/bin/$MACHTYPE:$PATH # make sure that ~/bin/i686 is on your path
$ export PATH=~/bin                 # make sure that ~/bin is on your path as well

7. Install ALLMAPS

$ mkdir code
$ cd code
$ git clone git://github.com/tanghaibao/jcvi.git     
$ export PYTHONPATH=/home/username/code:$PYTHONPATH  # make sure the directory is on your PYTHONPATH

8. Test sample data

$ wget https://www.dropbox.com/s/b497bi2b594m6fp/ALLMAPS-testdata.zip
$ unzip ALLMAPS-testdata.zip
$ cd ALLMAPS-testdata
$ sh run.sh