-#!/bin/sh
+#!/bin/bash
# Copyright (C) The Arvados Authors. All rights reserved.
#
# SPDX-License-Identifier: AGPL-3.0
-set -e
+set -e -o pipefail
-if test -z "$1" ; then
+if test -z "$1" -o -z "$2" ; then
echo "$0: Copies Arvados tutorial resources from public data cluster (jutro)"
- echo "Usage: copy-tutorial.sh <dest>"
- echo "<dest> is destination cluster configuration that can be found in ~/.config/arvados"
+ echo "Usage: copy-tutorial.sh <dest> <tutorial>"
+ echo "<dest> is 5-character cluster id of the destination"
+ echo "<tutorial> is which tutorial to copy, one of:"
+ echo " bwa-mem Tutorial from https://doc.arvados.org/user/tutorials/tutorial-workflow-workbench.html"
+ echo " whole-genome Whole genome variant calling tutorial workflow (large)"
exit
fi
-echo "Copying from public data cluster (jutro) to $1"
+src=jutro
+dest=$1
+tutorial=$2
-for a in $(cat $HOME/.config/arvados/$1.conf) ; do export $a ; done
+if ! test -f $HOME/.config/arvados/${dest}.conf ; then
+ echo "Please create $HOME/.config/arvados/${dest}.conf with the following contents:"
+ echo "ARVADOS_API_HOST=<${dest} host>"
+ echo "ARVADOS_API_TOKEN=<${dest} token>"
+ exit 1
+fi
+
+if ! test -f $HOME/.config/arvados/jutro.conf ; then
+ # Set it up with the anonymous user token.
+ echo "ARVADOS_API_HOST=jutro.arvadosapi.com" > $HOME/.config/arvados/jutro.conf
+ echo "ARVADOS_API_TOKEN=v2/jutro-gj3su-e2o9x84aeg7q005/22idg1m3zna4qe4id3n0b9aw86t72jdw8qu1zj45aboh1mm4ej" >> $HOME/.config/arvados/jutro.conf
+ exit 1
+fi
+
+for a in $(cat $HOME/.config/arvados/${dest}.conf) ; do export $a ; done
+
+echo
+echo "Copying from public data cluster (jutro) to $dest"
+echo
+
+make_project() {
+ name="$1"
+ owner="$2"
+ if test -z "$owner" ; then
+ owner=$(arv --format=uuid user current)
+ fi
+ project_uuid=$(arv --format=uuid group list --filters '[["name", "=", "'"$name"'"], ["owner_uuid", "=", "'$owner'"]]')
+ if test -z "$project_uuid" ; then
+ project_uuid=$(arv --format=uuid group create --group '{"name":"'"$name"'", "group_class": "project", "owner_uuid": "'$owner'"}')
+ link=$(arv link create --link '{"link_class": "permission", "name": "can_read", "tail_uuid": "'$dest'-j7d0g-anonymouspublic", "head_uuid": "'$project_uuid'"}')
+ fi
+ echo $project_uuid
+}
+
+copy_jobs_image() {
+ if ! arv-keepdocker | grep "arvados/jobs *latest" ; then
+ arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-4zz18-sxmit0qs6i9n2s4
+ fi
+}
+
+parent_project=$(make_project "Tutorial projects")
+copy_jobs_image
+
+if test "$tutorial" = "bwa-mem" ; then
+ echo
+ echo "Copying bwa mem tutorial"
+ echo
+
+ set -x
-project_uuid=$(arv --format=uuid group create --group '{"name":"User guide resources", "group_class": "project"}')
+ project_uuid=$(make_project 'User guide resources' $parent_project)
-# Bwa-mem workflow
-arv-copy --src jutro --dst $1 --project-uuid=$project_uuid f141fc27e7cfa7f7b6d208df5e0ee01b+59
-arv-copy --src jutro --dst $1 --project-uuid=$project_uuid jutro-7fd4e-mkmmq53m1ze6apx
+ # Bwa-mem workflow
+ arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-7fd4e-mkmmq53m1ze6apx
-echo "Data copied to \"User guide resources\" at $project_uuid"
+ set +x
+
+ echo
+ echo "Finished, data copied to \"User guide resources\" at $project_uuid"
+ echo "You can now go to Workbench and choose 'Run a process' and then select 'bwa-mem.cwl'"
+ echo
+fi
+
+if test "$tutorial" = "whole-genome" ; then
+ echo
+ echo "Copying whole genome variant calling tutorial"
+ echo
+
+ set -x
+
+ project_uuid=$(make_project 'WGS Processing Tutorial' $parent_project)
+
+ # WGS workflow
+ arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-7fd4e-tnxg9ytblbxm26i
+
+ set +x
+
+ echo
+ echo "Finished, data copied to \"WGS Processing Tutorial\" at $project_uuid"
+ echo "You can now go to Workbench and choose 'Run a process' and then select 'bwa-mem.cwl'"
+ echo
+fi
projects / arvados.git / blobdiff