Some SlackBuild scripts for Slackware.
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  1. PACKAGER'S README FOR OMERO-5.6.2
  2. Damien Goutte-Gattat <dgouttegattat@incenp.org>
  3. 1. DISCLAIMER
  4. This file does not come from the OMERO project and the OMERO
  5. developers don't endorse anything of it. Official documentation and
  6. instructions for installing and running OMERO server should be looked
  7. for at <https://docs.openmicroscopy.org/omero/5.6.2/sysadmins/index.html>.
  8. 2. SYSTEM USERS AND GROUPS
  9. The OMERO server installed by this SlackBuild is intended to be run
  10. by a dedicated `omero' user. That user will own most of the OMERO
  11. files and must also have a existing, writable HOME directory.
  12. The `doinst.sh' script will automatically create that user if it does
  13. not already exist in `/etc/passwd'. The new account will have a UID
  14. of 270, a HOME directory in `/var/lib/omero' and will belong to the
  15. `omero' group; that group will also be automatically created if
  16. needed.
  17. To use another UID/GID or another HOME directory, either edit the
  18. `doinst.sh' script before running the SlackBuild, or create the group
  19. and user yourself before installing the package.
  20. 3. INSTALLATION LAYOUT
  21. There are three locations on the filesystem that will be used by the
  22. package:
  23. - the OMERO main directory, `/opt/omero', where the programs and
  24. libraries themselves will be installed;
  25. - the `omero' user's home directory, by default `/var/lib/omero'
  26. (as created by the `doinst.sh' script, see above); it will hold
  27. some temporary files;
  28. - the data repository, where OMERO will store the raw data files,
  29. `/OMERO' by default.
  30. The three locations must be readable and writable by the `omero' user.
  31. The main directory is hardcoded in the SlackBuild and the associated
  32. scripts, but not in OMERO itself; you may change it if you want before
  33. running the SlackBuild.
  34. The `omero' user's home directory can be changed at any time with
  35. usermod(8). Restart OMERO for the change to take effect.
  36. The data repository is defined by the key `omero.data.dir' in the
  37. OMERO configuration.
  38. 4. OMERO CONFIGURATION AND CONTROL
  39. There are many parameters controlling OMERO's behavior, but most of
  40. them may be left unmodified for the first run. The only parameters
  41. that must be explicitly set before running OMERO are those defining
  42. the data repository (`omero.data.dir' and `omero.managed.dir') and
  43. the database backend (`omero.db.*').
  44. All parameters may be set by running the `omero config` command under
  45. the `omero` account. For example, to set the directory of the data
  46. repository:
  47. $ omero config set omero.data.dir /data/omero
  48. Parameters may also be defined in a `/etc/omero.conf` files, using
  49. the same format as the `omero.properties` file provided with OMERO.
  50. Starting and stoping OMERO is done with the `/etc/rc.d/rc.omero'
  51. control script. Before starting OMERO the first time, run
  52. `/etc/rc.d/rc.omero init'; the script will read the configuration
  53. file `/etc/omero.conf` if it exists and ensure the data repository
  54. and the database backend are ready to use (this includes
  55. automatically creating the PostgreSQL account and database if those
  56. specified in `/etc/omero/omero.properties' does not exist on the
  57. server). This initialization step should be performed each time the
  58. `/etc/omero.conf` is modified.
  59. 5. OMERO.web
  60. The Django-based web application OMERO.web is no longer packaged
  61. along with OMERO.server. Use the n/omero-web package to install it.
  62. Make sure Nginx and Django are installed. Add the following line to
  63. the OMERO configuration file /etc/omero.conf:
  64. ---8<----------------------------------------------------------------
  65. omero.web.application_server=wsgi
  66. --->8----------------------------------------------------------------
  67. Then, use the following command to produce a configuration snippet
  68. that can be directly inserted into the configuration of Nginx:
  69. omero web config nginx
  70. Start the web server, the OMERO server itself and the OMERO.web
  71. workers using the rc scripts provided in the corresponding packages.
  72. 6. BACKUP AND RESTORE
  73. There are two different items to backup:
  74. - the data directory (/OMERO by default, see 4. above);
  75. - the PostgreSQL database.
  76. The following commands backup everything into /backup:
  77. $ pg_dump -h localhost -U postgres -C omero > /backup/omero.sql
  78. $ rsync --archive --delete --compress --prune-empty-dirs \
  79. /OMERO /backup/omero.data
  80. To restore, copy the data files back to their locations and reload
  81. the database from the SQL dump.
  82. 7. UPGRADE
  83. For general informations about upgrading OMERO, see:
  84. http://www.openmicroscopy.org/site/support/omero5/sysadmins/server-upgrade.html
  85. To upgrade OMERO 5.5.x to OMERO-5.6.2:
  86. - Make sure you have Python3, as OMERO-5.6.x no longer supports Python2;
  87. - stop OMERO if it is running;
  88. - backup the SQL database;
  89. - upgrade the package;
  90. - start the upgraded server:
  91. # /etc/rc.d/rc.omero start