set -e -o pipefail
-if test -z "$1" -o -z "$2" ; then
+if test -z "$1" ; then
echo "$0: Copies Arvados tutorial resources from public data cluster (jutro)"
- echo "Usage: copy-tutorial.sh <dest> <tutorial>"
- echo "<dest> is 5-character cluster id of the destination"
+ echo "Usage: copy-tutorial.sh <tutorial>"
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
-src=jutro
-dest=$1
-tutorial=$2
-
-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
+if test -z "ARVADOS_API_HOST" ; then
+ echo "Please set ARVADOS_API_HOST to the destination cluster"
+ exit
fi
+src=jutro
+tutorial=$1
+
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
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 "Copying from public data cluster (jutro) to $ARVADOS_API_HOST"
echo
make_project() {
project_uuid=$(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
+ arv-copy --project-uuid=$parent_project jutro-4zz18-sxmit0qs6i9n2s4
fi
}
echo "Copying bwa mem tutorial"
echo
- set -x
-
- project_uuid=$(make_project 'User guide resources' $parent_project)
-
- # Bwa-mem workflow
- arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-7fd4e-mkmmq53m1ze6apx
-
- set +x
+ arv-copy --project-uuid=$parent_project jutro-j7d0g-rehmt1w5v2p2drp
echo
- echo "Finished, data copied to \"User guide resources\" at $project_uuid"
+ echo "Finished, data copied to \"User guide resources\" at $parent_project"
echo "You can now go to Workbench and choose 'Run a process' and then select 'bwa-mem.cwl'"
echo
fi
echo "Copying whole genome variant calling tutorial"
echo
- set -x
-
- project_uuid=$(make_project 'WGS Processing Tutorial' $parent_project)
-
- # WGS workflow
- arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-7fd4e-tnxg9ytblbxm26i
-
- set +x
+ arv-copy --project-uuid=$parent_project jutro-j7d0g-n2g87m02rsl4cx2
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 "Finished, data copied to \"WGS Processing Tutorial\" at $parent_project"
+ echo "You can now go to Workbench and choose 'Run a process' and then select 'WGS Processing Tutorial'"
echo
fi