Download

The latest stable release of pRESTO may be downloaded from PyPI or Bitbucket.

Development versions and source code are available on Bitbucket.

Installation

The simplest way to install the latest stable release of pRESTO is via pip:

> pip3 install presto --user

The current development build can be installed using pip and git in a similar fashion:

> pip3 install git+https://bitbucket.org/kleinstein/presto@master --user

If you currently have a development version installed, then you will likely need to add the arguments --upgrade --no-deps --force-reinstall to the pip3 command.

Requirements

• Python 3.4.0

• setuptools 2.0

• NumPy 1.8

• SciPy 0.14

• pandas 0.24

• Biopython 1.77

• AlignSets requires MUSCLE v3.8

• ClusterSets requires USEARCH v7.0, vsearch v2.3.2, or CD-HIT v4.6.8

• AssemblePairs-reference requires USEARCH v7.0 or BLAST+ 2.5

Linux

1. The simplest way to install all Python dependencies is to install the full SciPy stack using the instructions, then install Biopython according to its instructions.

2. Download the pRESTO bundle and run:

   > pip3 install presto-x.y.z.tar.gz --user
   

Mac OS X

1. Install Xcode, which is available from the Apple store or developer downloads.

2. Older versions Mac OS X will require you to install XQuartz 2.7.5, which is available from the XQuartz project.

3. Install Homebrew following the installation and post-installation instructions.

4. Install Python 3.4.0+ and set the path to the python3 executable:

   > brew install python3
   > echo 'export PATH=/usr/local/bin:$PATH' >> ~/.profile
   

5. Exit and reopen the terminal application so the PATH setting takes effect.

6. You may, or may not, need to install gfortran (required for SciPy). Try without first, as this can take an hour to install and is not needed on newer releases. If you do need gfortran to install SciPy, you can install it using Homebrew:

   > brew install gfortran
   

   If the above fails run this instead:

   > brew install --env=std gfortran
   

7. Install NumPy, SciPy, pandas and Biopython using the Python package manager:

   > pip3 install numpy scipy pandas biopython
   

8. Download the pRESTO bundle, open a terminal window, change directories to download location, and run:

   > pip3 install presto-x.y.z.tar.gz
   

Windows

1. Install Python 3.4.0+ from Python, selecting both the options ‘pip’ and ‘Add python.exe to Path’.

2. Install NumPy, SciPy, pandas and Biopython using the packages available from the Unofficial Windows binary collection.

3. Download the pRESTO bundle, open a Command Prompt, change directories to the download folder, and run:

   > pip install presto-x.y.z.tar.gz
   

4. For a default installation of Python 3.4, the pRESTO scripts will be installed into C:\Python34\Scripts and should be directly executable from the Command Prompt. If this is not the case, then follow step 5 below.

5. Add both the C:\Python34 and C:\Python34\Scripts directories to your %Path%. On Windows 7 the %Path% setting is located under Control Panel -> System and Security -> System -> Advanced System Settings -> Environment variables -> System variables -> Path.

6. If you have trouble with the .py file associations, try adding .PY to your PATHEXT environment variable. Also, opening a command prompt as Administrator and run:

   > assoc .py=Python.File
   > ftype Python.File="C:\Python34\python.exe" "%1" %*