Mercurial > repos > lldelisle > incucyte_stack_and_upload_omero

annotate upload_omero.sh @ 1:3c942429f610 draft default tip

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit de447190f0743b7f6a3b85e13f712fc07682af3c
author lldelisle
date Thu, 21 Dec 2023 17:04:46 +0000
parents e1cba36becb2
children
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e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
1 #!/bin/bash
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
2 omero_server="$1"
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
3 omero_user="$(cat $2 | awk 'NR==2{print $0}')"
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
4 omero_password="$(cat $2 | awk 'NR==3{print $0}')"
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
5 to_create=$3
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
6 screen_name_or_id=$4
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
7
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
8 if [ "$to_create" = "create" ]; then
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
9 # Create a screen:
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
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}')
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
11 echo "Just created the new screen ${screen_name_or_id}"
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
12 fi
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
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13
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
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14 echo "Start upload"
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
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15 companion_file=$(ls output/*.companion.ome)
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
16 omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} -T Screen:id:"${screen_name_or_id}" "${companion_file}" 2>&1
e1cba36becb2 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
lldelisle
parents:
diff changeset
17 echo "Upload finished"