X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a7631a1ccb6e2a6925d00a06562e171c4ce4ea2f..9b7a2816e223bd0cae3c9c69cf70afa74748a07d:/tools/copy-tutorial/copy-tutorial.sh

diff --git a/tools/copy-tutorial/copy-tutorial.sh b/tools/copy-tutorial/copy-tutorial.sh
index bdc75da2e1..6addeb1cda 100755
--- a/tools/copy-tutorial/copy-tutorial.sh
+++ b/tools/copy-tutorial/copy-tutorial.sh
@@ -1,25 +1,103 @@
-#!/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