Quick scripts for setting up Data Carpentry Genomics: https://datacarpentry.org/genomics-workshop/setup.html (option B)

00_README.md

Superceded by https://github.com/MonashBioinformaticsPlatform/data-carpentry-genomics-ansible

Quick scripts for setting up Data Carpentry Genomics: https://datacarpentry.org/genomics-workshop/setup.html (option B)

01_create_conda_env.sh

#!/bin/bash
# Based on: https://datacarpentry.org/genomics-workshop/setup.html (option B)
set -e

MINICONDA_PATH=$HOME/miniconda3-dc

if [[ "$(uname)" == "Darwin" ]]; then
  platform=MacOSX
  http_get_cmd="curl -O "
elif [[ "$(expr substr $(uname -s) 1 5)" == "Linux" ]]; then
  platform=Linux
  http_get_cmd=wget
fi

$http_get_cmd https://repo.anaconda.com/miniconda/Miniconda3-latest-${platform}-x86_64.sh
bash Miniconda3-latest-${platform}-x86_64.sh -b -p ${MINICONDA_PATH}
source ${MINICONDA_PATH}/bin/activate
conda init bash


conda create -n dc-genomics \
             -c bioconda \
             fastqc=0.11.7=5 \
             trimmomatic=0.38=0 \
             bwa=0.7.17=ha92aebf_3 \
             samtools=1.9=h8ee4bcc_1 \
             bcftools=1.8=h4da6232_3 \
             igv


conda activate dc-genomics

02_get_figshare_data.sh

#!/bin/bash
set -e
echo "ee17e9f2da7c12e065dee7a48f9a5721  dcdata.zip" >dcdata.zip.md5
wget -c -O dcdata.zip https://ndownloader.figshare.com/articles/7726454/versions/2
md5sum -c dcdata.zip.md5
unzip dcdata.zip
rm dcdata.zip

for f in *.tar.gz; do
  tar xvzf $f
done

for f in *.zip; do
  unzip $f
done

03_cleanup.sh

#!/bin/bash

mkdir -p .downloads
mv *.tar.gz .downloads/
mv *.zip .downloads/
rm dcdata.zip.md5
rm Miniconda*.sh