ckandoth

This guide will show you how to install conda and then use it to install nextflow and singularity for executing popular bioinformatics workflows. Unfortunately, singularity is not available on Windows or macOS. So, this guide will only target Linux environments. If you have to use Windows 10, then try WSL2. If you have to use macOS, then try a Virtual Machine.

Download the Miniconda3 installer for Linux environments:

curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh

Install into a folder named miniconda3 under your home directory, and delete the installer:

bash miniconda.sh -bup $HOME/miniconda3 && rm -f miniconda.sh

jrsa

$ 1 0.000005 0.2954511527092107 50 5 50
402 400 496 560 496 1 0\s0\s40\s-9\s0\s0\s0.5 0\s0\s40\s9\s0\s0\s0.5 0\s1\s-12.107891388002887\s0.49020072449645724\s100 0\s1\s-0.49020072449645724\s0.4899458951514504\s100 0\s1\s0\s0.4899458951514504\s100 0\s1\s-3.4423968860970877\s0.48994335934397704\s100 0\s1\s-8.969060690957324\s-4.088038007650795\s100 0\s-1\s0.48993828812503004\s-0.4896834587831105\s100 0\s-1\s0\s-0.4896834587831105\s100 0\s-1\s16.04076664862162\s-0.48993828812503004\s100 0\s-1\s0.0070150138786200245\s-0.02392429516405592\s100 0\s-1\s0\s-0.02392429516405592\s100 0\s-1\s9.993078392331174\s-0.0070150138786200245\s100 0\s1\s0\s0.48967838756419013\s100 0\s1\s-0.4899332169060475\s0.48967838756419013\s100 0\s1\s-6.996370694155912\s0.4899332169060475\s100 0\s1\s0\s-13.57798136396477\s100 0\s1\s0\s-8.999999996969999\s100
w 560 496 576 496 0
w 576 496 592 496 0
g 320 464 320 496 0
w 400 496 384 496 0
r 384 496 384 368 0 15000
r 544 368 544 432 0 1000000
w 544 432 544 464 1
R 544 368 544 336 0 0 40 9 0 0 0.5

isaiahtaylor

#!/bin/bash
set -e
function cleanup {
        echo ""
        echo "Cleaning up processes"
        kill -SIGINT -$GID
}
trap cleanup EXIT

if [ "$1" ]; then

vsoch

Bootstrap: localimage
From: /home/vanessa/.singularity/shub/deepvariant-docker-deepvariant:0.5.0.simg

# sregistry get gcr.io/deepvariant-docker/deepvariant:0.5.0
# sudo singularity build deepvariant Singularity

%environment
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    DV_GPU_BUILD=0
    export PATH DV_GPU_BUILD

ForgottenUmbrella

How to publish Python apps for human beings

So, you've created a Python app (be it a graphical user interface with Qt or the like, or a simple command line interface). Great! But how are others going to use it? Python applications often have dependencies (e.g. from third-party modules), and they also need a Python interpreter to run them. For a developer, installing all the necessary bits and bobs to make things work is okay, but that's unacceptable for a normal user - they just want to download the thing and run it.

Below are simple instructions to publish your app on the three main operating systems: Windows, macOS and Linux.

photocyte

>Illumina Single End Apapter 1					
ACACTCTTTCCCTACACGACGCTGTTCCATCT
>Illumina Single End Apapter 2					
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>Illumina Single End PCR Primer 1				
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina Single End PCR Primer 2				
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>Illumina Single End Sequencing Primer			
ACACTCTTTCCCTACACGACGCTCTTCCGATCT

pierrejoubert73

How to add a collapsible section in markdown

1. Example

Click me

Heading

1. Foo
2. Bar
   • Baz

• Qux

veuncent

Remote debugging in Docker (for Django apps)

In order to enable debugging for your Django app running in a Docker container, follow these steps using Visual Studio (Code):

1. Add ptvsd to your requirements.txt file

ptvsd == 4.3.2

2. To your launch.json, add this:

wassname

"""
Url: https://gist.github.com/wassname/1393c4a57cfcbf03641dbc31886123b8
"""
import unicodedata
import string

valid_filename_chars = "-_.() %s%s" % (string.ascii_letters, string.digits)
char_limit = 255

def clean_filename(filename, whitelist=valid_filename_chars, replace=' '):

JamesHagerman

How to get firmware onto mutable modules

I had the best luck with the Black Magic Probe and gdb.

Install compiler

First install the arm compiler:

sudo add-apt-repository ppa:team-gcc-arm-embedded/ppa