Difference between revisions of "Team:Waterloo/Software"

(Added and formatted instructions for PyMOL and PyRosetta installation on Windows.)
Line 19: Line 19:
 
<li><a href="https://www.python.org/downloads/">Download Python 2.7</a>. You MUST use the 64-bit version, and make sure to select the option to add python to your path.</li>
 
<li><a href="https://www.python.org/downloads/">Download Python 2.7</a>. You MUST use the 64-bit version, and make sure to select the option to add python to your path.</li>
 
<li>Install iPython. Open a command prompt, and type <code>python -m pip install ipython</code>. This should download and install ipython in one step.</li>
 
<li>Install iPython. Open a command prompt, and type <code>python -m pip install ipython</code>. This should download and install ipython in one step.</li>
−
<li>Get <a href="https://pypi.python.org/pypi/pyreadline/2.0">pyreadline</a> (Download the 64-bit version, pyreadline-2.0.win-amd64.exe). Run the exe once download is complete. This provides a bunch of tab-completion and other handy features, it isn't necessary, but is very helpful.</li>
+
<li><a href="https://pypi.python.org/pypi/pyreadline/2.0">Get pyreadline</a> (Download the 64-bit version, pyreadline-2.0.win-amd64.exe). Run the exe once download is complete. This provides a bunch of tab-completion and other handy features, it isn't necessary, but is very helpful.</li>
−
<li>Get a PyRosetta license. These are free for academic/non-commercial use. <a href="http://c4c.uwc4c.com/express_license_technologies/pyrosetta">Link</a>.</li>
+
<li> <a href="http://c4c.uwc4c.com/express_license_technologies/pyrosetta">Get a PyRosetta license</a>. These are free for academic/non-commercial use.</li>
 
<li>Once your license is processed (which should only take a couple minutes), you'll receive an email with a username and password, and a link to the download.</li>
 
<li>Once your license is processed (which should only take a couple minutes), you'll receive an email with a username and password, and a link to the download.</li>
 
<li>Download the most recent version of the PyRosetta windows. You'll want the .exe for the latest release.</li>
 
<li>Download the most recent version of the PyRosetta windows. You'll want the .exe for the latest release.</li>
Line 26: Line 26:
 
<li>Two shortcuts should appear on the desktop, one for "iPython PyRosetta shell" and on for "PyMOL PyRosetta Link". Delete the second one, as it doesn't work with the version of PyMOL we'll be using.</li>
 
<li>Two shortcuts should appear on the desktop, one for "iPython PyRosetta shell" and on for "PyMOL PyRosetta Link". Delete the second one, as it doesn't work with the version of PyMOL we'll be using.</li>
 
<li>Open the ipython shell using the remaining shortcut. type:
 
<li>Open the ipython shell using the remaining shortcut. type:
 +
<pre><code>from rosetta import *
 +
rosetta.init()
 +
</code></pre>
 +
<li>If you get a message ending with something like the following, you've successfully installed PyRosetta.
 +
<pre><code>core.init.random: RandomGenerator:init: Normal mode, seed=-1088387864 RG_type=mt19937</code></pre></li>
 +
</ol>
 +
 +
<p>PyMOL</p>
 +
 +
<p>Adapted from <a href="http://www.pymolwiki.org/index.php/Windows_Install#Pre-compiled_PyMOL">this guide</a></p>
 +
 +
<ol>
 +
<li>Create a folder (e.g. C:\PyMOL_Install) to hold the files>
 +
<li><a href="http://www.lfd.uci.edu/~gohlke/pythonlibs/">Download</a>:
 
<ul>
 
<ul>
−
    <li>from rosetta import *</li>
+
<li>pymol-1.7.6.0-cp27-none-win_amd64.whl</li>
−
    <li>rosetta.init()</li>
+
<li>pymol_launcher-1.0-cp27-none-win_amd64.whl</li>
 +
<li>numpy-1.9.2+mkl-cp27-none-win_amd64.whl</li>
 +
<li>Pmw-2.0.0-py2-none-any.whl</li></li>
 
</ul>
 
</ul>
−
<li>If you get a message ending with something like the following, you've successfully installed PyRosetta.
+
<li>Move the files to the folder you created.</li>
−
<p><code>core.init.random: RandomGenerator:init: Normal mode, seed=-1088387864 RG_type=mt19937</code></p></li>
+
<li>Start a command prompt, and move to the directory you saved the files in:
 +
<pre><code>cd C:\PyMOL_Install</code></pre></li>
 +
<li>Assuming you added python to you path earlier, run the command:
 +
<pre><code>python -m pip install --no-index --find-link="%CD%" --pre pymol_launcher-1.0-cp27-none-win_amd64.whl</code></pre>
 +
<ol>
 +
<li>If there are errors, try installing the .whl files in this order: <em>numpy</em>, <em>Pmw</em>, <em>pymol-1.7.6.0</em>, <em>pymol_launcher</em></li>
 +
<li>If there are no errors, you should be able start PyMOL using C:\Python27\PyMOL.exe</li>
 +
</ol>
 +
<li>Create a shortcut on your desktop to make starting PyMOL easier.</li>
 +
</ol>
 +
<p>Linking PyMOL and PyRosetta</p>
 +
<p>Adapted from <a href="http://www.pyrosetta.org/pymol_mover-tutorial">this guide</a>.</p>
 +
<ol>
 +
<li>Start PyMOL</li>
 +
<li>In the command line (upper window), type
 +
    <pre><code>run C:\Program Files\PyRosetta\PyMOLPyRosettaServer.py</code></pre></li>
 +
<li>You should see a message just above saying:
 +
<pre><code>
 +
    PyMOL <---> PyRosetta link started!
 +
    at 127.0.0.1 port 65000</code></pre>
 +
If it doesn't work, check if PyRosetta installed to the above path (which it should have if you followed the instructions on this page). If the path is different, modify the run command to match.</li>
 +
<li>Go to the 'File' menu and select 'Edit pymolrc'.</li>
 +
<li>Add the same run command to the file, then save it. This will start the PyRosetta link automatically every time you run PyMOL.</li>
 +
</ol>
  
 
     </section>
 
     </section>

Revision as of 00:28, 18 September 2015

Software

Mathematical Modelling

Give an overview of our GitHub code here.

PyRosetta and PyMOL

Windows Installation

PyRosetta

Adapted from this guide.

PyRosetta is fairly simple to install on Windows, assuming Python is installed. However, it does take large amounts of RAM (you'll need a computer with >4GB), so you may need to use the Linux version for older computers.

  1. Download Python 2.7. You MUST use the 64-bit version, and make sure to select the option to add python to your path.
  2. Install iPython. Open a command prompt, and type python -m pip install ipython. This should download and install ipython in one step.
  3. Get pyreadline (Download the 64-bit version, pyreadline-2.0.win-amd64.exe). Run the exe once download is complete. This provides a bunch of tab-completion and other handy features, it isn't necessary, but is very helpful.
  4. Get a PyRosetta license. These are free for academic/non-commercial use.
  5. Once your license is processed (which should only take a couple minutes), you'll receive an email with a username and password, and a link to the download.
  6. Download the most recent version of the PyRosetta windows. You'll want the .exe for the latest release.
  7. When the download completes, run the exe to install PyRosetta.
  8. Two shortcuts should appear on the desktop, one for "iPython PyRosetta shell" and on for "PyMOL PyRosetta Link". Delete the second one, as it doesn't work with the version of PyMOL we'll be using.
  9. Open the ipython shell using the remaining shortcut. type: 
    from rosetta import *
rosetta.init()
  10. If you get a message ending with something like the following, you've successfully installed PyRosetta. 
    core.init.random: RandomGenerator:init: Normal mode, seed=-1088387864 RG_type=mt19937

PyMOL

Adapted from this guide

  1. Create a folder (e.g. C:\PyMOL_Install) to hold the files>
  2. Download:
    • pymol-1.7.6.0-cp27-none-win_amd64.whl
    • pymol_launcher-1.0-cp27-none-win_amd64.whl
    • numpy-1.9.2+mkl-cp27-none-win_amd64.whl
    • Pmw-2.0.0-py2-none-any.whl
  3. Move the files to the folder you created.
  4. Start a command prompt, and move to the directory you saved the files in: 
    cd C:\PyMOL_Install
  5. Assuming you added python to you path earlier, run the command: 
    python -m pip install --no-index --find-link="%CD%" --pre pymol_launcher-1.0-cp27-none-win_amd64.whl
    1. If there are errors, try installing the .whl files in this order: numpy, Pmw, pymol-1.7.6.0, pymol_launcher
    2. If there are no errors, you should be able start PyMOL using C:\Python27\PyMOL.exe
  6. Create a shortcut on your desktop to make starting PyMOL easier.

Linking PyMOL and PyRosetta

Adapted from this guide.

  1. Start PyMOL
  2. In the command line (upper window), type 
    run C:\Program Files\PyRosetta\PyMOLPyRosettaServer.py
  3. You should see a message just above saying: 
    
    PyMOL <---> PyRosetta link started!
    at 127.0.0.1 port 65000
    If it doesn't work, check if PyRosetta installed to the above path (which it should have if you followed the instructions on this page). If the path is different, modify the run command to match.
  4. Go to the 'File' menu and select 'Edit pymolrc'.
  5. Add the same run command to the file, then save it. This will start the PyRosetta link automatically every time you run PyMOL.

Lab Team Calculators

Digest Calculator Ligation Calculator

Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honour such "nuggets" of computational work.

If you are working on software as your main project, please join the software track. If you are creating software as an addition to your main project, please apply for this award.

Here are a few examples from previous teams:

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