danielecook

# Generate data dictionary

DESCRIPTIONS <- list(mpg = "Miles Per Gallon")

# data dict function
data_dict <- function(data, descriptions = NA, print_table = FALSE){
  # Adapted from https://github.com/pw2/Data-Dictionary-Function/blob/master/Data%20Dictionary%20Function.R
  if(!require(pacman)) install.packages("pacman")
  pacman::p_load('tidyverse', 'psych', 'ggpubr', 'gridExtra', 'knitr', 'data.table')
  

danielecook

# ipinfo.io
# Retrieve information on your IP address

# JSON response 
curl ipinfo.io

# Retrieve just the IP address
curl ipinfo.io/ip

# Retrieve the hostname

danielecook

{
    for i in `seq 1 22`; 
        do echo ${i};
    done;
    echo "X";
    echo "Y";
    echo "MT";
} > names.txt

danielecook

import groovy.json.JsonOutput

json_param_file = "${workflow.projectDir}/pipeline_info/params.json"
new File(json_param_file).withWriter('utf-8') {
    writer ->
    def json_params = JsonOutput.prettyPrint(JsonOutput.toJson(params));
    writer.write(json_params);
}

danielecook

# docker build --file manta.Dockerfile -t swantonlab/manta .
FROM continuumio/miniconda3
RUN apt-get update && apt-get install -y procps
RUN conda config --add channels defaults && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge
RUN conda create -n manta bioconda::manta=1.6.0 && conda clean -a
ENV PATH /opt/conda/envs/manta/bin:$PATH
RUN conda env export --name manta > manta.yml

danielecook

 fd --extension bam --change-older-than "2020-02-26 00:00:00" | head -n 100

danielecook

# This script will download, index, and prep reference genomes.

# Prep N2 reference genome
RELEASE=WS274
PROJECT=PRJNA13758

mkdir -p "${PROJECT}.${RELEASE}" && cd "${PROJECT}.${RELEASE}"

# Annotation file
wget ftp://ftp.ensembl.org/pub/current_gff3/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.99.gff3.gz

danielecook

ag -o params\\.[A-Za-z\_0-9]+ *.nf | sort | uniq

danielecook

function test_igv {
    cat - > test.${1}
    igvtools index test.${1}
}

danielecook

# https://stackoverflow.com/questions/10312521/how-to-fetch-all-git-branches
git branch -r | grep -v '\->' | while read remote; do git branch --track "${remote#origin/}" "$remote"; done
git fetch --all
git pull --all