Installation

Operating System

XYalign has been tested on Linux and Mac operating systems, but has not been tested on Windows. This isn’t to say it won’t work, however we are unprepared to offer any Windows support at this time.

Requirements

XYalign has a number of required Python packages and external programs:

Python: 2.7

Python packages:
        matplotlib
        numpy
        pandas
        pybedtools
        pysam
        scipy

External Programs:
        bbmap (XYalign uses repair.sh and shuffle.sh from this suite of tools)
        bedtools
        bwa
        platypus
        sambamba
        samtools

Note

Bedtools is required for pybedtools and must be added to one’s PATH. XYalign will check that it is available by calling bedtools. Other external programs do not, however, need to be on one’s PATH and can be provided to XYalign using the appropriate flag(s):

--repairsh_path
--shufflesh_path
--bwa_path
--platypus_path
--samtools_path
--sambamba_path

Obtaining XYalign

We strongly recommend users install and manage all packages and programs using Anaconda. To do so:

1. First download and install either Anaconda or Miniconda (both work well, Miniconda is a lightweight version of Anaconda).

• Be sure to allow Anaconda to append to your PATH (it will ask for permission to do so during installation)

  • You can check this after installation with the command (from the command line):

    which python
    

  which should point you to the python installed in your Anaconda or Miniconda directory.

2. Linux and Mac users can finish installation with the following commands (note that \ indicates a continuation of the command on the next line):

   conda config --add channels r
   
   conda config --add channels defaults
   
   conda config --add channels conda-forge
   
   conda config --add channels bioconda
   
   conda create -n xyalign_env xyalign
   

This assumes you’re installing into a new environment called “xyalign_env”.

Note

You need to add channels in this order. Doing so will ensure priority of channels will go in the order bioconda > conda-forge > defaults > r. This is important because the source of bzip2 (required for many programs) needs to be conda-forge (the version in defaults will cause many programs to miss a required library).

You can then load the new environment (containing all required programs and packages) with:

source activate xyalign_env

To use Bioconda to simply install XYalign into your current environment, load the channels in using the commands listed above and then type:

conda install xyalign

In all cases, this will install XYalign, its dependancies, and all external programs that it calls.

Pip

XYalign can also be installed using pip, a tool used for installing Python packages, with the command:

pip install xyalign

However, note that this will not install any external programs that XYalign calls on for its various functions.