ILRI Research Computing

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====== Pasta ======
Practical Alignment using SATe and Transitivity.

===== Information =====

  * Latest version: git-d939adb2
  * Added: October, 2018
  * Link: https://github.com/smirarab/pasta

===== Usage =====

See versions of Pasta that are available:
<code>$ module avail pasta</code>

Load one version into your environment and run it:
<code>$ module load pasta/git-d939adb2
$ run_pasta.py -i input_fasta [-t starting_tree]</code>

Consult the [[https://github.com/smirarab/pasta/blob/master/pasta-doc/pasta-tutorial.md|Pasta tutorial]] for more information.

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

Note that the Pasta project does not tag their releases, so I've used the git commit hash at the time of installation.