kuang-da

Introduction

This gist is a note about install nvidia-docker in Pop!_OS 20.10. nvidia-docker is used to help docker containers compute on GPU.

The basic installcation is in Nvidia's offical documentation. But there are a few tweaks to make it work on Pop!_OS 20.10.

Setting up Docker

No surprise. Follow the offical documentaion should work.

Setting up NVIDIA Container Toolkit

sirselim

Jetson Xavier basecalling notes

initial basecalling runs

'fast' flip-flop calling on the Jetson Xavier

guppy_basecaller --disable_pings --compress_fastq -c dna_r9.4.1_450bps_fast.cfg -i flongle_fast5_pass/ -s flongle_test2 -x 'auto' --recursive 

nvictus

"""Run Length Encoding utilities for NumPy arrays.

Authors
-------
- Nezar Abdennur
- Anton Goloborodko

"""
from __future__ import division, print_function
import numpy as np

magnetikonline

Bash string manipulation cheatsheet

Assignment
Assign value to variable if variable is not already set, value is returned. Combine with a : no-op to discard/ignore return value.	${variable="value"} : ${variable="value"}

zachcp

#!/usr/bin/env python
"""
Modified from: 
https://github.com/chapmanb/bcbb/blob/master/align/adaptor_trim.py
See Also:
https://bcbio.wordpress.com/2009/08/09/trimming-adaptors-from-short-read-sequences/

Trim adaptor sequences from reads; designed for short read sequencing.

Allows trimming of adaptor sequences from a list of SeqRecords produced

markjlorenz

Reverse Port Tunneling with EC2

Reverse port tunneling is used to give a user outside of a networks firewall accesst to a computer inside the firewall where direct SSH connections aren't allowed. It works by the in-firewall computer SSH'ing to a middleman computer that then forwards incomming SSH connections on a given port to the firewalled computer.

Setup the middleman

• Get an ubuntu EC2 instance
• Download it's security keys (both in-firewall and out-firewall computers will need the private key)
• Setup the security group to allow connections on port 10002
• SSH into the middleman and add: GatewayPorts yes to /etc/ssh/sshd_config