Merge branch '21543-lightning-subdir'

[lightning.git] / example-su92l-1kg.sh

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
deleted file mode 100755 (executable)
index 7bd631b..0000000
--- a/example-su92l-1kg.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/bash
-
-set -ex
-
-PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
-go install
-lightning build-docker-image
-arv keep docker lightning-runtime
-
-project=su92l-j7d0g-jzei0m9yvgauhjf
-gvcf=su92l-4zz18-ykpcoea5nisz74f
-fasta=su92l-4zz18-s3e6as6uzsoocsb
-tags=su92l-4zz18-92bx4zjg5hgs3yc
-
-unfiltered=$(
-    lightning import       -project ${project} \
-       -tag-library ${tags}/tagset.fa.gz \
-       ${fasta})
-unfiltered=su92l-4zz18-fcyucnod8y4515p/library.gob
-filtered=$(
-    lightning filter       -project ${project} \
-       -i ${unfiltered} \
-       -min-coverage 0.9 -max-variants 30)
-numpy=$(
-    lightning export-numpy -project ${project} \
-       -i ${filtered})
-pca=$(
-    lightning pca          -project ${project} \
-       -i ${numpy})
-plot=$(
-    lightning plot         -project ${project} \
-       -i ${pca} \
-       -labels-csv ${gvcf}/sample_info.csv \
-       -sample-fasta-dir ${fasta})
-echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
-echo ${plot%%/*}