diff upload_omero.sh @ 1:9be687213bc9 draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero commit 39c8ae77d15d77ddcd8a0bb70f46d1be1531e9cc

--- a/upload_omero.sh	Thu Dec 12 12:42:20 2024 +0000
+++ b/upload_omero.sh	Fri Dec 13 07:58:28 2024 +0000
@@ -8,13 +8,13 @@
 
 if [ "$to_create" = "both" ]; then
     # Create a project:
-    project_name_or_id=$(${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Project name="${project_name_or_id}" | awk -F ":" 'END{print $NF}')
+    project_name_or_id=$(omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Project name="${project_name_or_id}" | awk -F ":" 'END{print $NF}')
     echo "Just created the new project ${project_name_or_id}"
 fi
 if [ "$to_create" = "both" ] || [ "$to_create" = "dataset" ]; then
-    dataset_name_or_id=$(${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Dataset name="${dataset_name_or_id}" | awk -F ":" 'END{print $NF}')
+    dataset_name_or_id=$(omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Dataset name="${dataset_name_or_id}" | awk -F ":" 'END{print $NF}')
     echo "Just created the new dataset ${dataset_name_or_id}"
-    ${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new ProjectDatasetLink parent=Project:${project_name_or_id} child=Dataset:${dataset_name_or_id}
+    omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new ProjectDatasetLink parent=Project:${project_name_or_id} child=Dataset:${dataset_name_or_id}
 fi
 echo "Start upload"
 omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} --depth 1 -T Dataset:id:"${dataset_name_or_id}" output 2>&1