Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
smarten [2020/03/06 10:25]
Jaroslaw Zola
smarten [2020/03/25 12:59] (current)
Jaroslaw Zola
Line 40: Line 40:
 ==== Software Specification ==== ==== Software Specification ====
  
-Jeston ​Nano comes with its own variant of Ubuntu Linux for Tegra – the specific version is ''​Ubuntu 18.04.4 LTS (GNU/Linux 4.9.140-tegra aarch64)''​. Since this is fully functional Linux, we have access to all common tools, including compilers, like ''​gcc''​ and ''​clang'',​ and the entire NVIDIA CUDA development environment (currently we are using ''​CUDA 10.0''​).+Jetson ​Nano comes with its own variant of Ubuntu Linux for Tegra – the specific version is ''​Ubuntu 18.04.4 LTS (GNU/Linux 4.9.140-tegra aarch64)''​. Since this is fully functional Linux, we have access to all common tools, including compilers, like ''​gcc''​ and ''​clang'',​ and the entire NVIDIA CUDA development environment (currently we are using ''​CUDA 10.0''​).
  
 Of course, the key requirement is to be able to run Oxford Nanopore tools. ONT provides MinKNOW framework in its repository. Just running fairly standard chain of Debian/​Ubuntu ''​apt''​ commands brings in all tools (notice that we are using ''​xenial''​ repository):​ Of course, the key requirement is to be able to run Oxford Nanopore tools. ONT provides MinKNOW framework in its repository. Just running fairly standard chain of Debian/​Ubuntu ''​apt''​ commands brings in all tools (notice that we are using ''​xenial''​ repository):​
Line 50: Line 50:
 ''​apt install minknow-core-minit-offline ont-bream4-minit ont-configuration-customer-minit ont-minknow-frontend-minit ont-minknow-static-frontend''​ ''​apt install minknow-core-minit-offline ont-bream4-minit ont-configuration-customer-minit ont-minknow-frontend-minit ont-minknow-static-frontend''​
  
-The only caveat is that currently, it is not possible to install ''​guppy''​ basecaller directly from packages (there are several reasons: first, dependencies that cannot be satisfied without downgrading Ubuntu, second, lack of support for NVIDIA SM53 in the default package). However, we were able to easily bypass these problems by compiling (with bit of editing) ''​guppy''​ from sources (we will share the process soon). Below is a glimpse at MinKNOW running on NVIDIA Nano.+The only caveat is that currently, it is not possible to install ''​guppy''​ basecaller directly from packages (there are several reasons: first, dependencies that cannot be satisfied without downgrading Ubuntu, second, lack of support for NVIDIA SM53 in the default package). However, we were able to easily bypass these problems by compiling (with bit of editing) ''​guppy''​ from sources (we will share the process soon). Below is a glimpse at MinKNOW running on NVIDIA Nano.
  
 {{ ::​2020-03-06_09.52.53-1.jpg?​300 |}} {{ ::​2020-03-06_09.52.53-1.jpg?​300 |}}
  • Show page