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Add script to download methyl files #415

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merged 7 commits into from
Jul 17, 2023
Merged

Add script to download methyl files #415

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cc226ea
add script to download methyl files
zzgeng Jul 10, 2023
a036ff8
update download-methyl.sh based on comments
zzgeng Jul 12, 2023
c2f35c9
update readme
zzgeng Jul 12, 2023
c8b1e9f
fix a typo
zzgeng Jul 12, 2023
4a84a75
Updating the code to pull the md5sum first, put the files into the di…
jharenza Jul 14, 2023
8fd67f9
uncomment release folder check
jharenza Jul 14, 2023
0ce5bbb
set base directories based on comment
zzgeng Jul 17, 2023
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31 changes: 31 additions & 0 deletions scripts/download_methyl.sh
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Original file line number Diff line number Diff line change
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#!/bin/bash

set -e
set -o pipefail

# download methylation files from the OpenPedCan data v12 data release s3 bucket

URL="https://d3b-openaccess-us-east-1-prd-pbta.s3.amazonaws.com/open-targets"
RELEASE="v13"

FILES=(`tr -s ' ' < ../data/$RELEASE/methyl-md5sum.txt | cut -d ' ' -f 2` release-notes.md)
for file in "${FILES[@]}"
do
if [ ! -e "../data/$RELEASE/$file" ]
then
echo "Downloading $file"
curl $URL/$RELEASE/$file -o ../data/$RELEASE/$file
fi
done

#check md5sum
cd ../data/$RELEASE
echo "Checking MD5 hashes..."
md5sum -c methyl-md5sum.txt
cd ../../

# Make symlinks in data/ to the files in the just downloaded release folder.
for file in "${FILES[@]}"
do
ln -sfn $RELEASE/$file data/$file
done
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