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INSTALL.md

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Installing Poplars

##For Linux To install Poplars on a Linux system, we recommend cloning the source code from this repository. If you do not have superuser privileges, you may install Poplars from the Python Package Index (pip).

###From Source

  1. Clone the GitHub repository

    kwade4@Jesry:~/git$ git clone https://github.com/PoonLab/Poplars.git
Cloning into 'Poplars'...
remote: Enumerating objects: 380, done.
remote: Counting objects: 100% (380/380), done.
remote: Compressing objects: 100% (226/226), done.
remote: Total 380 (delta 191), reused 309 (delta 143), pack-reused 0
Receiving objects: 100% (380/380), 30.65 MiB | 31.32 MiB/s, done.
Resolving deltas: 100% (191/191), done.

    This will create a directory (folder) called Poplars

  2. Navigate to the Poplars directory.

    Then run the setup.py installation script with superuser sudo privileges, which will install the package and the system-specific MAFFT binaries (executables) to /usr/local/lib. This allows you to use Poplars anywhere you can use Python!

    kwade4@Jesry:~/git$ cd Poplars
kwade4@Jesry:~/git/Poplars$ sudo python3 setup.py install
[sudo] password for kwade4: 
running install
running build
running build_py
[...]
Changing permissions of /usr/local/lib/python3.6/dist-packages/poplars/ref_genomes/K03455.fasta to 755
Changing permissions of /usr/local/lib/python3.6/dist-packages/poplars/ref_genomes/M33262.fasta to 755
Changing permissions of /usr/local/lib/python3.6/dist-packages/poplars/ref_genomes/HIV1_Mgroup.fasta to 755

###Using pip

  1. To install Poplars, check which version of Python is on your system:

       kwade4@Jesry:~$ python --version
   Python 2.7.15rc1
   kwade4@Jesry:~$ python3 --version
   Python 3.6.7

  2. Ensure that the Python Package Index is installed on your system. If you have Python 2, you will use pip or if you have Python 3, use pip3.

    There are 2 ways to check if pip or pip3 is installed:

    • Using the which command:

      If pip/pip3 installed on your system, the location of the pip/pip3 executable file(s) is displayed.

      kwade4@Jesry:~$ which pip3
/usr/bin/pip3

      If pip or pip3 is not installed on your system, nothing will be displayed this command will display nothing.

      kwade4@Jesry:~$ which pip3
kwade4@Jesry:~$

    • Using the pip -V or pip3 -V command:

      If pip is installed on your system, the version of pip will be displayed.

      kwade4@Jesry:~/git/Poplars$ pip3 -V 
pip 9.0.1 from /usr/lib/python3/dist-packages (python 3.6)

      If pip or pip3 is not installed on your system, an error message will be printed.

      kwade4@Jesry:~$ pip3 -V
pip3: command not found

    The exact output of these commands varies with the operating system. This example uses Ubuntu 18.0.4.

  3. If pip is not installed, you need to install pip using your system's package manager.
    For example, installing pip3 using Ubuntu 18.0.4:

    kwade4@Jesry:~$ sudo apt install python3-pip
[sudo] password for kwade4: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  dh-python libexpat1-dev libpython3-dev libpython3.6 libpython3.6-dev libpython3.6-minimal
  libpython3.6-stdlib python-pip-whl python3-dev python3-setuptools python3-wheel python3.6
  python3.6-dev python3.6-minimal
Suggested packages:
  python-setuptools-doc python3.6-venv python3.6-doc binfmt-support
The following NEW packages will be installed:
  dh-python libexpat1-dev libpython3-dev libpython3.6-dev python-pip-whl python3-dev python3-pip
  python3-setuptools python3-wheel python3.6-dev
The following packages will be upgraded:
  libpython3.6 libpython3.6-minimal libpython3.6-stdlib python3.6 python3.6-minimal
5 upgraded, 10 newly installed, 0 to remove and 189 not upgraded.
Need to get 53.1 MB of archives.
After this operation, 82.2 MB of additional disk space will be used.
Do you want to continue? [Y/n] y

    Enter y if you are ready to install pip3.

    Note that this step requires a network connection.

    ...

For Windows

To install Poplars on a Windows system, we recommend cloning the source code from this repository.

###From Source

  1. Ensure Git Bash is installed. You can check this by searching for "Git Bash" in the Start Menu.

  2. Once Git Bash is installed, clone or download the repository.