Mercurial > repos > mvdbeek > incucyte_stack_and_upload_omero_debug
diff upload_omero.sh @ 0:a599551e800d draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
| author | mvdbeek |
|---|---|
| date | Tue, 06 Aug 2024 15:28:26 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/upload_omero.sh Tue Aug 06 15:28:26 2024 +0000 @@ -0,0 +1,17 @@ +#!/bin/bash +omero_server="$1" +omero_user="$(cat $2 | awk 'NR==2{print $0}')" +omero_password="$(cat $2 | awk 'NR==3{print $0}')" +to_create=$3 +screen_name_or_id=$4 + +if [ "$to_create" = "create" ]; then + # Create a screen: + screen_name_or_id=$(omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Screen name="${screen_name_or_id}" | awk -F ":" 'END{print $NF}') + echo "Just created the new screen ${screen_name_or_id}" +fi + +echo "Start upload" +companion_file=$(ls output/*.companion.ome) +omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} -T Screen:id:"${screen_name_or_id}" "${companion_file}" 2>&1 +echo "Upload finished"