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2 Installation guide for ezBAMQC for from source installs
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3 =====================================================
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4
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5 When installing ezBAMQC there are several options, but the main point is: since ezBAMQC uses C++ STD 11 you'll need a version of GCC that can support that, this useally means 4.8 or 4.9. beyond that, you'll need Python, R and Corrplot for interfacing with the C code.
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6
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7 :Intallation:
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8 `Source Code <https://github.com/mhammell-laboratory/bamqc/archive/0.6.4.tar.gz>`_
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9
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10 `Pypi <https://pypi.python.org/pypi?:action=display&name=BAMQC&version=0.6.4>`_
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11
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12 :Prerequisites:
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13 * `python2.7 <https://www.python.org/download/releases/2.7/>`_
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14 * `R <https://www.r-project.org/>`_
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15 * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
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16 * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install
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17
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18 :Notes:
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19 * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
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20 * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers
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21 * `IUS <https://ius.io/>`_ for Python2.7
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22 * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
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23 * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
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24
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25 Setup
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26 =====
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27
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28 1) Make sure that the GCC comiler is in your PATH:
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29
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30 ::
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31
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32 export PATH=/path/to/gcc:$PATH
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33
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34 2) Make sure that python2.7 is in your PYTHONPATH:
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35
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36 ::
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37
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38 export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
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39
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40 3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup.
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41
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42 From Source
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43 ~~~~~~~~~~~
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44
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45 1) Download source
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46
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47 2) Unpack tarball and go to the directory of the package:
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48
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49 ::
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50
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51 tar xvfz bamqc-0.6.4.tar.gz
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52
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53 cd bamqc-0.6.4
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54
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55 3) Run make:
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56
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57 ::
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58
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59 make
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60
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61 From Setup.py
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62 ~~~~~~~~~~~~~
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63
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64 ::
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65
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66 python2.7 setup.py install
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67
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68 From Pypi
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69 ~~~~~~~~~
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70
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71 ::
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72
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73 pip2.7 install BAMqc
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74
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