Practical Alignment using SATe and Transitivity.
See versions of Pasta that are available:
$ module avail pasta
Load one version into your environment and run it:
$ module load pasta/git-d939adb2 $ run_pasta.py -i input_fasta [-t starting_tree]
Consult the Pasta tutorial for more information.
Notes from the sysadmin during installation:
$ cd /tmp $ mkdir pasta-code $ cd pasta-code $ git clone https://github.com/smirarab/pasta.git $ git clone https://github.com/smirarab/sate-tools-linux.git $ git clone https://github.com/kodicollins/pasta-databases sate-tools-linux/pasta-databases $ cd pasta $ sudo mkdir -p /export/apps/pasta/git-d939adb2/lib/python2.7/site-packages $ sudo chown -R aorth /export/apps/pasta/git-d939adb2 $ export PYTHONPATH=/export/apps/pasta/git-d939adb2/lib/python2.7/site-packages $ python setup.py develop --prefix=/export/apps/pasta/git-d939adb2 $ cd .. $ sudo cp -r sate-tools-linux/ /export/apps/pasta/git-d939adb2 $ sudo chown -R root:root /export/apps/pasta/git-d939adb2 # for graphical interface (use on HPC only to avoid installing stupid dependencies on nodes) $ sudo yum install wxPython.x86_64
Note that the Pasta project does not tag their releases, so I've used the git commit hash at the time of installation.