Task #1068
Import en ligne de commande
Status: | Closed | Start date: | 01/12/2015 | |
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Priority: | Normal | Due date: | ||
Assignee: | - | % Done: | 100% | |
Category: | - | |||
Target version: | - |
Description
Bonjour
Peut on avoir une procedure pour se servir d omero en ligne de commande?
merci
marc
History
#1 Updated by Volker Baecker over 9 years ago
On MAC and Linux you can use the script provided by OMERO:
1. Open a terminal and cd to the directory of you OMERO client installation, for example
cd ~/programs/OMERO.clients-5.0.0-ice35-b19.linux
2. Run the importer-cli script with the parameters you want, for example
./importer-cli -s omero.mri.cnrs.fr -u <username> -w <password> /my/folder/*
This will import all images in /my/folder
You can find more parameter to set for example the dataset, and so on, here:
http://www.openmicroscopy.org/site/support/omero5/users/command-line-import.html
There is no script for windows provided, however you can run the import in a similar way by directly using java:
java -Xmx512M -cp "./OmeroImporter.jar:./omero.insight.jar" -Djava.library.path="/home/baecker/programs/OMERO.clients-5.0.0-ice35-b19.linux" ome.formats.importer.cli.CommandLineImporter -s omero.mri.cnrs.fr -u <username> -w <password> /my/folder/*
You must replace the library path in the -Djava.library.path option with the path to the omero client installation on your machine.
#2 Updated by Volker Baecker over 9 years ago
CORRECTION:
The above java call uses linux style for the library options it should be
java -Xmx512M -cp "./OmeroImporter.jar;./omero.insight.jar" -Djava.library.path="/home/baecker/programs/OMERO.clients-5.0.0-ice35-b19.linux" ome.formats.importer.cli.CommandLineImporter -s omero.mri.cnrs.fr -u <username> -w <password> /my/folder/*
That is you should use a ; instead of the : to separate the jars in the classpath.
#3 Updated by Volker Baecker over 9 years ago
Here is the correct windows version:
java -Xmx512M -cp ".\OmeroImporter.jar;.\omero.insight.jar" -Djava.library.path="D:\Users\baecker\omero\OMERO.clients-5.0.6-ice35-b53.win" ome.formats.importer.cli.CommandLineImporter -s omero.mri.cnrs.fr -u <username> -w <password> ..\my\images\*
Note the use of ; and \.
The library path needs to point to your omero installation
#4 Updated by Volker Baecker about 9 years ago
- Status changed from New to Closed
- % Done changed from 0 to 100