COSMIC Data Downloader

cosmic_download.sh

username=your_username
password=your_password

auth_string=$(echo $username:$password | base64)
echo "# auth string: $auth_string"

cosmic_url=https://cancer.sanger.ac.uk/cosmic

# ===================
# get current version
# ===================
release=$(curl -s $cosmic_url/download | grep -oP 'Data Downloads \(release .+?\)')
current_version=$(echo $release | grep -oP 'v\d+')
echo "# current version: $current_version"


# ===================
# list file names
# ===================
files=$(curl -s $cosmic_url/download | grep -oP '"https://cancer.sanger.ac.uk/cosmic/file_download_info.+?"')
for file in $files;do
  echo ${file##*%2F} | cut -d '"' -f 1
done > file.list


# ===================
# get download url
# ===================
ref_versions="GRCh37 GRCh38"

for ref_version in $ref_versions;do
  echo mkdir $ref_version
  while read file;do
    url=$(
      curl -sH "Authorization: Basic $auth_string" $cosmic_url/file_download/$ref_version/cosmic/$current_version/$file |
      grep -oP '"https://.+"'
    )
    echo wget -c $url -O $ref_version/$file
  done < file.list
done