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.. _installation:
Installation
=======================
Dependencies
-----------------------
A compiler that supports C++11 is needed to build nanopolish. Development of the code is performed using `gcc-4.8 <https://gcc.gnu.org/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 <http://www.hdfgroup.org/HDF5/release/obtain5.html>`_ compiled with multi-threading support ``--enable-threadsafe``
* `eigen-3.2.5 <http://eigen.tuxfamily.org/>`_
* `htslib-1.4 <http://github.com/samtools/htslib>`_
Additionally the helper `scripts` require `biopython <http://biopython.org/>`_ and `pysam <http://pysam.readthedocs.io/en/latest/installation.html>`_.
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
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