Download & Installation¶
Development was done using gcc 9.3.0 on an Ubuntu 16.04 platform. While installation on other platforms is possible, Ubuntu is the platform that is recommended and supported.
Clone the DNAscent repository with the recursive flag so that the dependencies are cloned as well.
git clone --recursive https://github.com/MBoemo/DNAscent.git
The DNAscent directory will appear in your current directory. Switch to the latest release and compile the software by running:
cd DNAscent git checkout 2.0.2 make
This will put the DNAscent executable into the DNAscent/bin directory. Compilation requires a version of gcc that supports C++14, and a typical compile time for DNAscent and all of its dependencies is 5-7 minutes.
Cloning the repository recursively (see above) will provide all the required dependencies so you don’t need to find them yourself. For completeness, however, they are listed here:
- pfasta (https://github.com/kloetzl/pfasta)
- fast5 (https://github.com/mateidavid/fast5.git)
- htslib (https://github.com/samtools/htslib.git)
- hdf5lib (https://support.hdfgroup.org/HDF5/)
- tinydir (https://github.com/cxong/tinydir.git)
- TensorFlow (https://www.tensorflow.org/install/lang_c)
Please note that the high throughput sequencing library (htslib) requires bzlib and lzma for compression. While these are common on most systems, if you don’t have these, apt-get lzma-dev, liblzma-dev, and libbz2-dev. In addition, pfasta requires libbsd on Linux.
VBZ Fast5 Compression¶
In new versions of MinKNOW, the fast5 files are compressed with VBZ Compression (see https://github.com/nanoporetech/vbz_compression). To use DNAscent on these compressed fast5 files, do the following (N.B., we’re assuming you don’t have root permissions):
Go to https://github.com/nanoporetech/vbz_compression/releases and download the plugin appropriate for your processor architecture. In this example, we’ll use
Download and unpack the plugin:
wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz tar -xf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
Add the plugin to your path:
DNAscent detectas normal.
DNAscent detect executable can make use of a GPU, although this is optional (see Detect). DNAscent requires CUDA 10.0 and cuDNN 7.5, and information about these can be found at the following links:
- cuDNN: https://developer.nvidia.com/cudnn
- CUDA: https://developer.nvidia.com/cuda-10.0-download-archive
Always discuss any installation or version changes with your system administrator.