The first user which you will need to configure is the “root” OMERO user (different from any root-level Unix account). upgrade 5.0.5 to 5.1.1 omero.web forbidden OMERO.web running but status says not started¶ If you upgraded OMERO but forgot to stop OMERO.web, processes will still be running. In 2008, we presented our first overview of using OMERO for HCS data . Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Source
In the right-most pane, select Create Basic Task…. Unfortunately, at this point, the virtual machine screen goes black with only a non-blinking cursor. One account is used for running the OMERO server (either your own or one you created specially for running OMERO, referred to here as “omero_user”). Be sure to add HDF5 to the PATH for all users during the install.
If you installed Ice globally via your package manager, make sure you included ice-python. Click the Next button. I named mine OMERO.start.
This caused no problems. C:\Windows\system32>cd C:\OMERO.server C:\OMERO.server>bin\omero db script Traceback (most recent call last): File "C:\OMERO.server\bin\\omero", line 125, in
Created using Sphinx 1.2.3. [ome-users] ERROR: Could not import omero.cli! (No module named Ice) Shaun Hare Shaun.Hare at nottingham.ac.uk Mon Apr 25 17:49:26 BST 2016 Previous message: [ome-users] OMERO.webtagging 2.0.0 Release requirements Ice.Default.Host PRs to review for docs Blitz Gateway memory leak advice RFE: OMERO added to global PATH/PYTHONPATH Document CLI `--style json` minor API doc fix Open-ended version numbers CLI import Open the Server Manager by either clicking the icon in the Windows Taskbar or by selecting its shortcut in Start -> Administrative Tools. http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-April/005947.html The download link for jdk-7u51-windows-x64.exe is here: http://www.oracle.com/technetwork/java/javase/downloads/index.html I accepted all default options, including installing it to C:\Program Files\Java\jdk1.7.0_51. 3.2.2 Python 2.6.6 Python, besides being my choice scripting language, is also
gunicorn logs in var Server bugs Clarify Noise reduction Olympus ScanR fails to import OMERO reader out of blitz.jar Web bugs CLI: final naming decisions B-F possible PR for 5.1.x IAdmin Move the patch file into the same directory as mimetypes.py. numpy-MKL-1.8.1rc1.amd64-py2.6.exe from http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy scipy-0.13.3.win-amd64-py2.6.exe from http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy matplotlib-1.3.1.win-amd64-py2.6.exe from http://matplotlib.org/downloads.html I installed the packages in the above list in top-to-bottom order. The OMERO documentation recommends frequent backups of 1) the PostgreSQL database and 2) the OMERO binary data.
When scheduling a Windows task to automatically run the OMERO server at startup, I ensured that the task DID NOT stop if it ran for longer than three days. The second line appears roughly two seconds after the first appears. Open Microscopy Environment The OME community Skip to content Advanced search Search Products Documentation Home Products OMERO Bio-Formats OME-TIFF OME Files C++ Partner Projects Legacy Documentation OMERO Bio-Formats OME Model and In the future, once we're done testing the software, we'll probably upgrade the permissions to "Read-only." According to the OMERO documentation, administrators can't severe Read-only permissions on data if they're initially
With these two changes, the OMERO server documenation should lead to a working OMERO server. 4.3 Setting up routine backups Note: Windows Task Scheduler is the Windows equivalent to Unix's cron, this contact form Following this, I learned that an HDF5 install is ALSO required for PyTables. (Managing package dependencies on Windows sucks.) So I downloaded hdf5-1.8.12-win64-vs10shared.zip from http://www.hdfgroup.org/HDF5/release/obtain5.html, unzipped it, and ran the executable My computer system 2.1.2. the record-keeping that describes how our results are derived from our raw data.
However, as data volumes grow in size and complexity, more sophisticated systems are required to query, process and access complex, highly integrated and linked datasets. Directory exists but is not registered¶ Import errors of type Directory exists but is not registered: CheckedPath(username_id) suggest a server-side issue under the ManagedRepository. You should disable SSH X11-forwarding in your SSH session by using the -x flag as follows before you restart the OMERO.server: ssh -x my_server.examples.com OutOfMemoryError / PermGen space errors in OMERO.server have a peek here It installed Pillow 2.4.0 for Python 2.6 (64-bit).
Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. If nothing is listening on 4064, you may need to specify which network interface to use. I fixed it by adding ld_args.append('/MANIFEST') to below the line ld_args.append('/MANIFESTFILE:' + temp_manifest) in msvc9compiler.py, which is found in C:\Python26\Lib\disutils\.
This was because of a bug, either in the software or documentation, that asked that we enable 32-bit compatibility when in fact it prevented OMERO.web from displaying in a web browser. This batch file can be run atuomatically using Windows Task Scheduler. Review utils script OMEROPy TO DEPRECATE paths_to_object failing with ValueError: 1039354L is not in list CLI: review SkipHead processing OMERO may break with PostgreSQL 9.6 review paths_to_objects hql queries populate_metadata requires To resolve this, define the OMERO_TMPDIR environment variable to point at a temporary directory located on the local file system (e.g. /tmp/omero).
Additional Python libraries – See the OMERO.server installtion guide. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own Setting up routine backups 4.4. http://sinistro.org/could-not/could-not-import-the-clipboard-because.html Ice in Windows won't work with Python 2.7.
or with the OMERO.insight client. 2.1.4 Solution: Enabled Virtualization Support in the BIOS I solved the above problem by enabling virtualization support in my computer's BIOS. (I don't know why this