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1 pyPRADA installation
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2
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3 pyPRADA requires python 2.6 or 2.7, third party packages pysam and biopython.
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4
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5 1. Install python
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6 By default python is installed in Linux system. To check your python version, type
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7
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8 python -V
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9
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10 You may choose install python in your own directory, or ask your administrator to install it for you. Here below shows how to install python to your local directory.
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11 (1) download python
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12 $ wget http://www.python.org/ftp/python/2.7.2/Python-2.7.2.tgz
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13 (2) unzip
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14 $ tar zxfv Python-2.7.2.tgz
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15 (3) configure & make
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16 $ cd Python-2.7.2
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17 $ ./configure --prefix=/where/you/want/to/install
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18 $ make
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19 $ make install
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20 (4) add python path to your system path
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21 In B shell, edit .bashrc file in your home directory, add the following line
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22 export PATH=/python-dir/bin:$PATH
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23 In C shell, edit .cshrc file in your home directory, add the following line
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24 setenv PATH /python-dir/bin:$PATH
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25 To make the changes effective, source the .bashrc file or .cshrc file
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26 $ source .bashrc
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27
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28 Now check python version again. Python 2.7 should have been installed and set to be the default python.
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29
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30 2. Install third party packages
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31 (1) download pysam and biopython
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32 $ wget https://pysam.googlecode.com/files/pysam-0.6.tar.gz
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33 $ wget http://biopython.org/DIST/biopython-1.60.tar.gz
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34 (2) unzip files
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35 $ tar zxfv biopython-1.60.tar.gz
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36 $ tar zxfv pysam-0.6.tar.gz
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37 (3) configure / make
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38 $ cd biopython-1.60
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39 $ python setup.py install
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40 $ cd pysam-0.6
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41 $ python setup.py install
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42 (4) test
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43 You may leave the directories and test your package installations.
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44 $ cd
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45 $ python
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46 This brings you to the python interactive interface. Import the two packages, if no error occurs, your packages have been successfully installed. Otherwise, consult your administrator or someone with experiences with python.
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47
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48 >>> import pysam
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49 >>> import Bio
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50
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51 3. Install pyPRADA
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52 pyPRADA has been pre-compiled, thus does not require configure/make steps. To make it more convenient, we recommend to add its path to system path.
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53 First, unzip the package to the location you prefer. To add the path to system, see step 1.(4)
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54
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55 4. Test pyRADA
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56 To test pyPRADA, type the following command in your terminal. It will return a user manual for prada-fusion module.
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57
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58 $ prada-fusion
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59
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60 5. Help
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61 For assistance or bug report, contact Siyuan Zheng (szheng2@mdanderson.org) or Rahul Vegesna (RVegesna@mdanderson.org).
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62
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