Mercurial > repos > mvdbeek > incucyte_stack_and_upload_omero_debug
comparison 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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| -1:000000000000 | 0:a599551e800d |
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| 1 #!/bin/bash | |
| 2 omero_server="$1" | |
| 3 omero_user="$(cat $2 | awk 'NR==2{print $0}')" | |
| 4 omero_password="$(cat $2 | awk 'NR==3{print $0}')" | |
| 5 to_create=$3 | |
| 6 screen_name_or_id=$4 | |
| 7 | |
| 8 if [ "$to_create" = "create" ]; then | |
| 9 # Create a screen: | |
| 10 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}') | |
| 11 echo "Just created the new screen ${screen_name_or_id}" | |
| 12 fi | |
| 13 | |
| 14 echo "Start upload" | |
| 15 companion_file=$(ls output/*.companion.ome) | |
| 16 omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} -T Screen:id:"${screen_name_or_id}" "${companion_file}" 2>&1 | |
| 17 echo "Upload finished" |