Installation¶

This pipeline was build upon many dependencies and Python code. Therefore there was the need to use a package/environment manager. For this task we highly recommend CONDA . The following installation instructions assume the user wants to install and use CONDA. If you already have any recent conda distribution on your system do not use the Quick install Guide, as it will install Miniconda. If you do not which to use CONDA please look at all the dependencies needed to use SNAPPy in the ‘environment.yaml’ file.

Quick install Guide - Linux and Windows 10 (With Windows subsystem for Linux)¶

This instalation was tested on Ubuntu 16 and 18 LTS as well as Windows 10 With ubuntu 18 terminal. Do not use this method if you already have conda installed on your computer.

Download of clone SNAPPy from here and put it in a desired location:
```
git clone https://github.com/PMMAraujo/snappy
```
Open a terminal and move to the downloaded folder:
```
cd snappy
```

Give permission to the snappy installation script to run, and run it:

chmod +x linux_snappy_installer_x86_64.sh
./linux_snappy_installer_x86_64.sh

This task is time consuming and may take several minutes.

After the SNAPPy’s dependencies installation a series of tests will be executed using pytest. Please ensure no errors occur.
1. If there was any errors clean the downloaded folder and start from step 1. If the problem persist please try to follow the Install point-by-point - Linux and Windows 10 (With Windows subsystem for Linux). If you are still unable to install SNAPPy after this contact us to EMAIL.
SNAPPy is now ready to use! When you want to use SNAPPy open a new terminal inside SNAPPy’s folder and activate the conda environment by typing:
```
conda activate snappy
```

For a quick start on SNAPPy’s usage look at the Tutorials section. Note: In certain systems you may need to give premission to new files you insert inside the SNAPPy folder, for instance new sequences to subtype (chmod +x input/new_seqeunces.fasta).

Quick install Guide - macOS 10¶

This instalation was tested on macOS 10.14 (Mojave). Do not use this method if you already have conda installed on your computer.

Download of clone SNAPPy from here and put it in a desired location:
```
git clone https://github.com/PMMAraujo/snappy
```
Open a terminal and move to the downloaded folder:
```
cd snappy
```

Give permission to the snappy installation script to run, and run it:

chmod +x macos_snappy_installer_x86_64.sh
./macos_snappy_installer_x86_64.sh

This task is time consuming and may take several minutes.

After the SNAPPy’s dependencies installation a series of tests will be executed using pytest. Please ensure no errors occur.
1. If there was any errors clean the downloaded folder and start from step 1. If the problem persist please try to follow the Install point-by-point - macOS 10. If you are still unable to install SNAPPy after this contact us to EMAIL.
SNAPPy is now ready to use! When you want to use SNAPPy open a new terminal inside SNAPPy’s folder and activate the conda environment by typing:
```
conda activate snappy
```

For a quick start on SNAPPy’s usage look at the Tutorials section. Note: In certain systems you may need to give premission to new files you insert inside the SNAPPy folder, for instance new sequences to subtype (chmod +x input/new_seqeunces.fasta).

Install point-by-point - macOS 10¶

This instalation was tested on macOS 10.14 (Mojave).

Open a terminal, download Miniconda3 version 4.6.14 and install it:

wget https://repo.continuum.io/miniconda/Miniconda3-4.6.14-MacOSX-x86_64.sh -O ./miniconda.sh
bash ./miniconda.sh -b -p $HOME/miniconda

This task may take several minutes.

Download or clone SNAPPy from here and put it in a desired location:
```
git clone https://github.com/PMMAraujo/snappy
```
Move to the downloaded folder:
```
cd snappy
```

Activate conda and add it tho the bash paths:

source ~/miniconda/etc/profile.d/conda.sh
conda init

Note: It is not actually needed to add conda path to the bash path but it makes it easier to use.

Create SNAPPy’s conda environment:
```
conda-env create -f environment.yaml
```
Activate SNAPPy’s conda environment:
```
conda activate snappy
```
Run the tests to ensure the installation was successful. Please ensure no errors occur:
```
py.test
```
SNAPPy is now ready to use! When you want to use SNAPPy open a new terminal inside SNAPPy’s folder and activate the conda by typing:
```
conda activate snappy
```

For a quick start on SNAPPy’s usage look at the Tutorials section. Note: In certain systems you may need to give premission to new files you insert inside the SNAPPy folder, for instance new sequences to subtype (chmod +x input/new_seqeunces.fasta).

Install point-by-point - Linux and Windows 10 (With Windows subsystem for Linux)¶

This instalation was tested on Ubuntu 16 and 18 LTS as well as Windows 10 With ubuntu 18 terminal.

Open a terminal, download Miniconda3 version 4.6.14 and install it:

wget https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O ./miniconda.sh
bash ./miniconda.sh -b -p $HOME/miniconda

This task may take several minutes.

Download or clone SNAPPy from here and put it in a desired location:
```
git clone https://github.com/PMMAraujo/snappy
```
Move to the downloaded folder:
```
cd snappy
```

Activate conda and add it tho the bash paths:

source ~/miniconda/etc/profile.d/conda.sh
conda init

Note: It is not actually needed to add conda path to the bash path but it makes it easier to use.

Create SNAPPy’s conda environment:
```
conda-env create -f environment.yaml
```
Activate SNAPPy’s conda environment:
```
conda activate snappy
```
Run the tests to ensure the installation was successful. Please ensure no errors occur:
```
py.test
```
SNAPPy is now ready to use! When you want to use SNAPPy open a new terminal inside SNAPPy’s folder and activate the conda by typing:
```
conda activate snappy
```

For a quick start on SNAPPy’s usage look at the Tutorials section. Note: In certain systems you may need to give premission to new files you insert inside the SNAPPy folder, for instance new sequences to subtype (chmod +x input/new_seqeunces.fasta).