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tomwhite / cubed-example.ipynb
Created April 18, 2024 11:46
Flox groupby example using Cubed
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tomwhite / mackerel.ipynb
Created December 30, 2023 11:06
Which station on the London Tube map doesn't share any letters with "mackerel"?
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tomwhite / hail_on_spark2.sh
Created February 9, 2017 10:25
Minimal Hail using Spark 2
git clone https://github.com/hail-is/hail
cd hail
./gradlew installDist
./gradlew shadowJar
function hail() {
num_executors=$1
shift
spark2-submit \
--master yarn-client \
--driver-memory 3G \
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tomwhite / hail_exac.txt
Created October 14, 2016 14:00
Load ExAC in Hail as variant annotations
# Raw data is here: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/
# In particular: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz
# Use Hail to annotate: https://github.com/broadinstitute/hail/blob/master/docs/ImportAnnotations.md#AnnoVar
# Query from Impala. This ties in to the Omics use case, which is to enable access from multiple Hadoop tools.
# Build Hail
gradle clean shadowJar