Installation¶

Dependencies¶

A compiler that supports C++11 is needed to build nanopolish. Development of the code is performed using gcc-4.8.

By default, nanopolish will download and compile all of its required dependencies. Some users however may want to use system-wide versions of the libraries. To turn off the automatic installation of dependencies set HDF5=noinstall, EIGEN=noinstall or HTS=noinstall parameters when running make as appropriate. The current versions and compile options for the dependencies are:

libhdf5-1.8.14 compiled with multi-threading support --enable-threadsafe
eigen-3.2.5
htslib-1.4

Additionally the helper scripts require biopython and pysam.

Installing the latest code from github (recommended)¶

You can download and compile the latest code from github as follows

git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
make

Installing a particular release¶

When major features have been added or bugs fixed, we will tag and release a new version of nanopolish. If you wish to use a particular version, you can checkout the tagged version before compiling

git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
git checkout v0.7.1
make

To run using docker¶

First build the image from the dockerfile:

docker build .

Note the uuid given upon successful build. Then you can run nanopolish from the image:

docker run -v /path/to/local/data/data/:/data/ -it :image_id  ./nanopolish eventalign -r /data/reads.fa -b /data/alignments.sorted.bam -g /data/ref.fa