arichardson

Ninja support for CLion IDE (working with newer versions of clion)

This script enables Ninja-powered builds in CLion IDE by wrapping around CMake, which it uses. See my blog post for details.

Disclaimer

This script is provided AS IS with no guarantees given or responsibilities taken by the author. This script relies on undocumented features of CLion IDE and may lead to instability of build and/or IDE. Use it on your own risk under WTFPL terms.

hghwng

pkg/
src/
understand-bin-*.pkg.*
Understand-*.tgz
.SRCINFO

marcelm

#!/usr/bin/env python3
"""
Mask low-quality bases in a FASTQ file with 'N'.
Adjust cutoff_front and cutoff_back below to use
different thresholds (currently: 20 at 5' end,
0 at 3' end).

Usage:
  python3 qualmask.py input.fastq.gz > output.fastq

darencard

Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.

Extracting paired FASTQ read data from a BAM mapping file

Sometimes FASTQ data is aligned to a reference and stored as a BAM file, instead of the normal FASTQ read files. This is okay, because it is possible to recreate raw FASTQ files based on the BAM file. The following outlines this process. The useful software samtools and bedtools are both required.

From each bam, we need to extract:

1. reads that mapped properly as pairs
2. reads that didn’t map properly as pairs (both didn’t map, or one didn’t map)

ctb

banded kraken - example usage

Prepare the database:

mkdir ecoli_many_sigs
cd ecoli_many_sigs
curl -O -L https://github.com/dib-lab/sourmash/raw/master/data/eschericia-sigs.tar.gz
tar xzf eschericia-sigs.tar.gz
cd ../

kahlos

# Script to silently install MATLAB components, run as root if installing to /opt
# Requires: `license.lic`, `packages` list and `file-install-key` files

# Download license.lic and create file-install-key file from [MATLAB license centre](https://uk.mathworks.com/licensecenter/licenses)
# Download and extract latest [MATLAB installer](https://uk.mathworks.com/downloads/)
# Download packages `archive` files by running installer graphically first
# Make a package list, uncommenting lines from installer_input, `tail -87 installer_input.txt > packages`
# Check destination directories are correct below

# Destination, MATLAB installer and config files directory

jchandra74

Pimping Up Your PowerShell & Cmder with Posh-Git, Oh-My-Posh, & Powerline Fonts

Backstory (TLDR)

I work as a full-stack developer at work. We are a Windows & Azure shop, so we are using Windows as our development platform, hence this customization.

For my console needs, I am using Cmder which is based on ConEmu with PowerShell as my shell of choice.

Yes, yes, I know nowadays you can use the Linux subsystem on Windows 10 which allow you to run Ubuntu on Windows. If you are looking for customization of the Ubuntu bash shell, check out this article by Scott Hanselman.

trinker

dat <- data.frame(
    freq = c(37, 88, 47, 89, 28, 68, 65, 98, 68, 86, 50, 87, 59, 82, 45, 65, 52, 32, 59, 47, 68, 78, 39, 31, 64, 68)
)

dat[["sector"]] <- rep(c("U.S. adults", "AAAS scientist"), nrow(dat)/2)

field <- c("Biomedical sciences", "Climate, energy, space sciences")
dat[["field"]] <- factor(rep(field, c(10, 16)), levels=field)

items <-  c(

hkmix

#include <iostream>
#include <iomanip>
#include <random>
#include <string>
#include <thread>
#include <vector>

using std::size_t;

class Point {

slopp

snippet gg
	ggplot(${1:data}, aes(${2:aes})) + 
	  geom_${3:geom}()

snippet shiny
	library(shiny)
	ui <- fluidPage(
		${1:ui}
	)