Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add script to download methyl files #415

Merged
merged 7 commits into from
Jul 17, 2023
Merged

Add script to download methyl files #415

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -160,6 +160,7 @@ _Note: the `download-data.sh` script now has the ability to skip downloads of un
Once this has been done, run `bash download-data.sh` to acquire the latest release.
This will create symlinks in `data/` to the latest files.
It's safe to re-run `bash download-data.sh` to check that you have the most recent release of the data.
For downloading DNA methylation-related data, run `bash download-methyl.sh` in `scripts` folder.
We will update the default release number whenever we produce a new release.

### Data Access via CAVATICA
Expand Down
51 changes: 51 additions & 0 deletions scripts/download-methyl.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
#!/bin/bash

set -e
set -o pipefail

# download methylation files from the OpenPedCan data v13 data release s3 bucket

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

# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"

# If RUN_LOCAL is used, the time-intensive steps are skipped because they cannot
# be run on a local computer -- the idea is that setting RUN_LOCAL=1 will allow for
# local testing running/testing of all other steps
RUN_LOCAL=${RUN_LOCAL:-0}

# Get base directory of project
cd ..
BASEDIR="$(pwd)"
cd -

# check if the release folder exists, if not, create a release folder
[ ! -d "$BASEDIR/data/$RELEASE/" ] && mkdir $BASEDIR/data/$RELEASE/

# The md5sum file provides our single point of truth for which files are in a release.
curl --create-dirs $URL/$RELEASE/methyl-md5sum.txt -o $BASEDIR/data/$RELEASE/methyl-md5sum.txt -z $BASEDIR/data/$RELEASE/methyl-md5sum.txt

FILES=(`tr -s ' ' < $BASEDIR/data/$RELEASE/methyl-md5sum.txt | cut -d ' ' -f 2` release-notes.md)

for file in "${FILES[@]}"
do
if [ ! -e "$BASEDIR/data/$RELEASE/$file" ]
then
echo "Downloading $file"
curl --create-dirs $URL/$RELEASE/$file -o $BASEDIR/data/$RELEASE/$file
fi
done

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

# 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
Loading