Browse Source

n/omero: Upgraded to omero-5.0.5.

slackware-14.2
Damien Goutte-Gattat 7 years ago
parent
commit
f9fb6b6517
9 changed files with 51 additions and 93 deletions
  1. +0
    -1
      n/omero/OMERO.server-5.0.2-ice35-b26.zip.sha1
  2. +1
    -0
      n/omero/OMERO.server-5.0.5-ice35-b47.zip.sha1
  3. +28
    -41
      n/omero/README
  4. +1
    -15
      n/omero/doinst.sh
  5. +6
    -15
      n/omero/omero.SlackBuild
  6. +10
    -16
      n/omero/rc.omero
  7. +0
    -1
      xap/omero-client/OMERO.clients-5.0.2-ice35-b26.linux.zip.sha1
  8. +1
    -0
      xap/omero-client/OMERO.clients-5.0.5-ice35-b47.linux.zip.sha1
  9. +4
    -4
      xap/omero-client/omero-client.SlackBuild

+ 0
- 1
n/omero/OMERO.server-5.0.2-ice35-b26.zip.sha1 View File

@ -1 +0,0 @@
29bd94066b2aa539f3a2dad6fe8144e10c82365f OMERO.server-5.0.2-ice35-b26.zip

+ 1
- 0
n/omero/OMERO.server-5.0.5-ice35-b47.zip.sha1 View File

@ -0,0 +1 @@
4f1b8de024f4e7aae4ca02e4843307913fac6752 OMERO.server-5.0.5-ice35-b47.zip

+ 28
- 41
n/omero/README View File

@ -1,4 +1,4 @@
PACKAGER'S README FOR OMERO-5.0.2
PACKAGER'S README FOR OMERO-5.0.5
Damien Goutte-Gattat <dgouttegattat@incenp.org>
@ -30,38 +30,30 @@
3. INSTALLATION LAYOUT
There are four locations on the filesystem that will be used by the
There are three locations on the filesystem that will be used by the
package:
- the OMERO main directory, `/opt/omero', where the programs and
libraries themselves will be installed;
- the OMERO configuration directory, `/etc/omero', will store all
the configuration files; they should normally be in OMERO's main
directory, but I prefer to have them in `/etc', so I symlink
`/opt/omero/etc' to `/etc/omero' to allow OMERO to find them;
- the `omero' user's home directory, by default `/var/lib/omero'
(as created by the `doinst.sh' script, see above); it will hold
some temporary files and the current runtime configuration of
OMERO, if different from the default built-in configuration;
some temporary files;
- the data repository, where OMERO will store the raw data files,
`/OMERO' by default.
The four locations must be readable by the `omero' user; the main
directory, the `omero' user's home directory, and the data repository
must be writable by that user.
The three locations must be readable and writable by the `omero' user.
The main and configuration directories are hardcoded in the
SlackBuild and the associated scripts, but not in OMERO itself; you
may change them if you want before running the SlackBuild.
The main directory is hardcoded in the SlackBuild and the associated
scripts, but not in OMERO itself; you may change it if you want before
running the SlackBuild.
The `omero' user's home directory can be changed at any time with
usermod(8). Restart OMERO for the change to take effect.
The data repository is defined by the key `omero.data.dir' in the
main configuration file `/etc/omero/omero.properties'.
OMERO configuration.
Note that OMERO 5.0.0 needs another directory, defined by the key
`omero.managed.dir'. In the default configuration file, this key
@ -84,18 +76,26 @@
them may be left unmodified for the first run. The only parameters
that must be explicitly set before running OMERO are those defining
the data repository (`omero.data.dir' and `omero.managed.dir') and
the database backend (`omero.db.*'), in
`/etc/omero/omero.properties'.
the database backend (`omero.db.*').
All parameters may be set by running the `omero config` command under
the `omero` account. For example, to set the directory of the data
repository:
$ omero config set omero.data.dir /data/omero
Parameters may also be defined in a `/etc/omero.conf` files, using
the same format as the `omero.properties` file provided with OMERO.
Starting and stoping OMERO is done with the `/etc/rc.d/rc.omero'
control script. Before starting OMERO the first time, run
`/etc/rc.d/rc.omero init'; the script will read the configuration
files and ensure the data repository and the database backend are
ready to use (this includes automatically creating the PostgreSQL
account and database if those specified in
`/etc/omero/omero.properties' does not exist on the server). This
initialization step should be performed each time a configuration
file is modified.
file `/etc/omero.conf` if it exists and ensure the data repository
and the database backend are ready to use (this includes
automatically creating the PostgreSQL account and database if those
specified in `/etc/omero/omero.properties' does not exist on the
server). This initialization step should be performed each time the
`/etc/omero.conf` is modified.
5. OMERO.web
@ -104,7 +104,7 @@
as it requires some configuration.
Add the following lines to the OMERO configuration file
/etc/omero/omero.properties:
/etc/omero.conf:
---8<----------------------------------------------------------------
omero.web.application_server=fastcgi-tcp
@ -175,9 +175,7 @@
6. BACKUP AND RESTORE
There are three different items to backup:
- configuration settings in /etc/omero/;
There are two different items to backup:
- the data directory (/OMERO by default, see 4. above);
@ -190,8 +188,8 @@
/OMERO /backup/omero.data
To restore, copy the configuration and data files back to their
locations and reload the database from the SQL dump.
To restore, copy the data files back to their locations and reload
the database from the SQL dump.
7. UPGRADE
@ -213,17 +211,6 @@
$ cd /opt/omero
$ psql -h localhost -U omero omero < sql/psql/OMERO5.0__0/OMERO4.4__0.sql
- check config files in /etc/omero; remove old config file
/etc/omero/grid/default.xml and apply new settings:
# /etc/rc.d/rc.omero init
- start the upgraded server:
# /etc/rc.d/rc.omero start
WARNING: The last version of this SlackBuild (5.0.2-2GGD) now uses the
Ice-3.5 build of OMERO. When upgrading from a previous package that
provided the Ice-3.4 build, you need to 1) upgrade d/ice as well up to
at least ice-3.5.1, and 2) after upgrading OMERO and before restarting
the server, delete the /opt/omero/var/registry directory.

+ 1
- 15
n/omero/doinst.sh View File

@ -1,18 +1,4 @@
#!/bin/sh
config()
{
NEW="$1"
OLD="`dirname $NEW`/`basename $NEW .new`"
if [ ! -r $OLD ]; then
mv $NEW $OLD
elif [ "`cat $OLD | md5sum`" = "`cat $NEW | md5sum`" ]; then
rm $NEW
fi
}
for f in backup.cfg hibernate.properties ice.config internal.cfg ivysettings.xml logback-cli.xml logback-indexing-cli.xml logback-indexing.xml logback.xml master.cfg node1.cfg node2.cfg omero.properties rollover.cfg testdropbox.config grid/default.xml grid/templates.xml ; do
config /etc/omero/$f.new
done
if ! grep ^omero /etc/group > /dev/null ; then
/usr/sbin/groupadd -g 270 omero
@ -24,4 +10,4 @@ if ! grep ^omero /etc/passwd > /dev/null ; then
chown omero:omero /var/lib/omero
fi
chown -R omero /opt/omero /etc/omero
chown -R omero /opt/omero

+ 6
- 15
n/omero/omero.SlackBuild View File

@ -29,8 +29,8 @@
# Source package infos
NAMESRC=${NAMESRC:-OMERO.server}
VERSION=${VERSION:-5.0.2}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice35-b26.zip}
VERSION=${VERSION:-5.0.5}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice35-b47.zip}
WGET=${WGET:-http://downloads.openmicroscopy.org/omero/$VERSION/artifacts/$ARCHIVE}
# Build infos
@ -69,20 +69,11 @@ sha1sum -c $ARCHIVE.sha1
mkdir -p $PKG/opt
cd $PKG/opt
unzip $CWD/$ARCHIVE
mv OMERO.server-$VERSION-ice35-b26 omero
mv OMERO.server-$VERSION-ice35-b47 omero
rm omero/bin/*.bat
# Install config files in /etc/omero
mkdir -p $PKG/etc
mv omero/etc $PKG/etc/omero
ln -s /etc/omero $PKG/opt/omero/etc
(
cd $PKG/etc/omero
rm -rf Windows.cfg env.bat env.sh local.properties.example grid/windefault.xml nginx.conf.*
for f in backup.cfg hibernate.properties ice.config internal.cfg ivysettings.xml logback* master.cfg node?.cfg omero.properties rollover.cfg testdropbox.config grid/*.xml ; do
mv $f $f.new
done
)
rm omero/etc/{Windows.cfg,apache.conf.template,env.bat,env.sh,local.properties.example}
rm omero/etc/nginx.conf.*
rm omero/etc/grid/windefault.xml
# Install launch scripts
install -D -m 755 $CWD/omero.sh $PKG/usr/bin/omero


+ 10
- 16
n/omero/rc.omero View File

@ -1,32 +1,26 @@
#!/bin/bash
DB_ROOT=postgres
CONFIG_FILE=/etc/omero/omero.properties
CONFIG_FILE=/etc/omero.conf
ICEGRID_PIDFILE=/opt/omero/var/master/master.pid
OMERO_WEB_ENABLED=no
case "$1" in
init)
if [ ! -f $CONFIG_FILE ]; then
echo Configuration file $CONFIG_FILE not found! Aborting...
exit 1
if [ -f $CONFIG_FILE ]; then
echo Loading configuration
sudo -H -u omero -i omero config load $CONFIG_FILE
fi
echo Reseting previous configuration
rm -f ${CONFIG_FILE%/omero.properties}/grid/config.xml
echo Reading configuration from $CONFIG_FILE...
DATADIR=$(sed -nre 's/^omero\.data\.dir=(.*)$/\1/p' $CONFIG_FILE)
DB_HOST=$(sed -nre 's/^omero\.db\.host=(.*)$/\1/p' $CONFIG_FILE)
DB_PORT=$(sed -nre 's/^omero\.db\.port=(.*)$/\1/p' $CONFIG_FILE)
CONFIG=$(sudo -H -u omero -i omero config get)
DATADIR=$(echo "$CONFIG" | sed -nre 's/^omero\.data\.dir=(.*)$/\1/p')
DB_HOST=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.host=(.*)$/\1/p')
DB_PORT=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.port=(.*)$/\1/p')
[ -n "$DB_PORT" ] || DB_PORT=5432
DB_NAME=$(sed -nre 's/^omero\.db\.name=(.*)$/\1/p' $CONFIG_FILE)
DB_USER=$(sed -nre 's/^omero\.db\.user=(.*)$/\1/p' $CONFIG_FILE)
DB_NAME=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.name=(.*)$/\1/p')
DB_USER=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.user=(.*)$/\1/p')
PGOPTS="-h $DB_HOST -p $DB_PORT -U $DB_ROOT"
echo Applying configuration...
sudo -H -u omero -i omero config load $CONFIG_FILE
if [ ! -d $DATADIR ]; then
echo Creating data repository...
mkdir -p $DATADIR


+ 0
- 1
xap/omero-client/OMERO.clients-5.0.2-ice35-b26.linux.zip.sha1 View File

@ -1 +0,0 @@
862af9d1467e9a93a5e4fed82bc56a88efd0f973 OMERO.clients-5.0.2-ice35-b26.linux.zip

+ 1
- 0
xap/omero-client/OMERO.clients-5.0.5-ice35-b47.linux.zip.sha1 View File

@ -0,0 +1 @@
98408a2c84bb6372375d3ffc1e3d151400700d52 OMERO.clients-5.0.5-ice35-b47.linux.zip

+ 4
- 4
xap/omero-client/omero-client.SlackBuild View File

@ -27,13 +27,13 @@
# Source package infos
NAMESRC=${NAMESRC:-OMERO.clients}
VERSION=${VERSION:-5.0.2}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice35-b26.linux.zip}
VERSION=${VERSION:-5.0.5}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice35-b47.linux.zip}
WGET=${WGET:-http://downloads.openmicroscopy.org/omero/$VERSION/artifacts/$ARCHIVE}
# Build infos
NAMEPKG=${NAMEPKG:-omero-client}
BUILD=${BUILD:-2GGD}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
EXT=${EXT:-txz}
@ -62,7 +62,7 @@ if [ ! -r $ARCHIVE ]; then
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$NAMESRC-$VERSION-ice35-b26.linux
NAME=$NAMESRC-$VERSION-ice35-b47.linux
# Extract and install
mkdir -p $PKG/usr/lib


Loading…
Cancel
Save