Web site:

the authentification is achieved via Google SDK (e.g. 301.0.0)

tar xfz google-cloud-sdk-301.0.0-linux-x86_64.tar.gz
cd google-cloud-sdk
# to gain a bit flexibility by not using the awkward browser (Konqueror) at CSD3
gcloud auto login --no-launch-browser
# to set PROJECT_ID=divine-aegis-278909
gcloud config set divine-aegis-278909

followed by gsutil config where gsutil is installed via virtualenv as follows,

module load python/3.7
virtualenv py37
source py37/bin/activate
pip install gsutil==4.50
cd ${dir}/py37/bin
gsutil ls
# gsutil cp test gs::/covid19-hg-upload-bugbank
gsutil cp test gs://covid19-hg-upload-uk--blood-donors-cohort

Less useful is the usual way to install.

tar xvfz gsutil.tar.gz -C ..
cd ../gsutil
pip install pyasn1==0.4.8  --user
python install --prefix=$HPC_WORK




The GWAS summary statistics from R7 public data can be downloaded as follows,

gsutil -m cp -r \
  "gs://finngen-public-data-r7/summary_stats" \

and with all results lined up together we could use

gsutil -m cp -r \
  "gs://finngen-public-data-r7/annotations" \
  "gs://finngen-public-data-r7/covid" \
  "gs://finngen-public-data-r7/finemapping" \
  "gs://finngen-public-data-r7/summary_stats" \

This could be very space hungry and we could make a list of files and select by phenocode, e.g.,

gsutil ls gs://finngen-public-data-r7/summary_stats > finngen-r7.list
grep -e JUVEN_ARTHR -e L12_PSORIASIS -e D3_SARCOIDOSIS finngen-r7.list | \
xargs -l -I {} gsutil -m cp {} .

The phenocode can be found from


The GTEx v8 QTL resources,

gsutil -m cp -r \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/" \

or Europeans individually,

gsutil -m cp -r \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_EUR_eQTL_all_associations/" \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_EUR_sQTL/" \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_EUR_sQTL_all_associations/" \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_eQTL_all_associations/" \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_sQTL/" \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_sQTL_all_associations/" \
  "gs://gtex-resources/GTEx_Analysis_v8_QTLs/GTEx_Analysis_v8_sQTL_leafcutter_counts.tar" \

as described here,



Exerpts of scripts,

# setup
# Request an account
# upload
  gsutil ls gs://covid19-hg-upload-uk--blood-donors-cohort
  gsutil -m cp $1 gs://covid19-hg-upload-uk--blood-donors-cohort
  gsutil -m cp 20210317*/output/INTERVAL.Zhao* gs://covid19-hg-upload-uk--blood-donors-cohort
# web:
# HGI spreadsheet
  ls 20210317*/output/INTERVAL.Zhao* | xargs -l basename | xsel -i
# Fill the form (now uses tab in the spreadsheet),
# HGI results
# gs://covid19-hg-analysis
# gs://covid19-hg-public
# Bugbank
# gsutil cp $1 gs://covid19-hg-upload-bugbank