Mercurial > repos > mvdbeek > incucyte_stack_and_upload_omero_debug

annotate upload_omero.sh @ 1:6df9ac33bb91 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 16:04:29 +0000
parents a599551e800d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
1 #!/bin/bash
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
2 omero_server="$1"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
3 omero_user="$(cat $2 | awk 'NR==2{print $0}')"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
4 omero_password="$(cat $2 | awk 'NR==3{print $0}')"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
5 to_create=$3
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
6 screen_name_or_id=$4
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
7
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
8 if [ "$to_create" = "create" ]; then
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
9 # Create a screen:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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}')
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
11 echo "Just created the new screen ${screen_name_or_id}"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
12 fi
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
13
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
14 echo "Start upload"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
15 companion_file=$(ls output/*.companion.ome)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
17 echo "Upload finished"