Browse Source

n/omero: Upgraded to omero-5.1.0.

slackware-14.2
Damien Goutte-Gattat 7 years ago
parent
commit
1e027ce1b2
  1. 1
      n/omero/OMERO.server-5.0.8-ice35-b60.zip.sha1
  2. 1
      n/omero/OMERO.server-5.1.0-ice35-b40.zip.sha1
  3. 72
      n/omero/README
  4. 10
      n/omero/omero.SlackBuild
  5. 3
      n/omero/omero.sh
  6. 18
      n/omero/rc.omero

1
n/omero/OMERO.server-5.0.8-ice35-b60.zip.sha1

@ -1 +0,0 @@
2b9f6f7def2e142cce93fb635e7d0a7fcb402e40 OMERO.server-5.0.8-ice35-b60.zip

1
n/omero/OMERO.server-5.1.0-ice35-b40.zip.sha1

@ -0,0 +1 @@
2e51d82f4efb542ea6ef311a855d9106bee56090 OMERO.server-5.1.0-ice35-b40.zip

72
n/omero/README

@ -1,4 +1,4 @@
PACKAGER'S README FOR OMERO-5.0.8
PACKAGER'S README FOR OMERO-5.1.0
Damien Goutte-Gattat <dgouttegattat@incenp.org>
@ -8,7 +8,7 @@
This file does not come from the OMERO project and the OMERO
developers don't endorse anything of it. Official documentation and
instructions for installing and running OMERO server should be looked
for at <http://www.openmicroscopy.org/site/support/omeror5/sysadmins/>.
for at <http://www.openmicroscopy.org/site/support/omero5/sysadmins/>.
2. SYSTEM USERS AND GROUPS
@ -55,20 +55,6 @@
The data repository is defined by the key `omero.data.dir' in the
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
uses the value of the `omero.data.dir' key as follows:
omero.data.dir=/OMERO/
omero.managed.dir=${omero.data.dir}/ManagedRepository
but OMERO then complains that `omero.data.dir' is undefined, so you
should really specify a full path for `omero.managed.dir`, even if
the directory is located below `omero.data.dir`:
omero.data.dir=/OMERO/
omero.managed.dir=/OMERO/ManagedRepository
4. OMERO CONFIGURATION AND CONTROL
@ -124,53 +110,13 @@
Then, you need to install and configure the Apache HTTP server to
actually serve the application.
NOTE: Do *not* follow the official OMERO documentation from this
point, as it does not support running OMERO.web with Apache 2.4 and
the mod_proxy_fcgi module. In particular, the configuration lines
produced by the following command:
omero web config apache
are not suitable for Apache 2.4.
Instead, add the following stanza to your Apache configuration:
---8<----------------------------------------------------------------
RewriteEngine On
RewriteRule ^/?$ /omero/ [R]
ProxyPass /webclient fcgi://localhost:4080
ProxyPass /webadmin fcgi://localhost:4080
Alias /static /opt/omero/lib/python/omeroweb/static
<Directory "/opt/omero/lib/python/omeroweb/static">
Options -Indexes +FollowSymLinks
Require all granted
</Directory>
--->8----------------------------------------------------------------
(Make sure the mod_rewrite, mod_proxy and mod_proxy_fcgi modules are
loaded. This is normally done in the default httpd configuration file
provided by Slackware.)
The following command will produce a configuration snippet that can
directly inserted into the configuration file of Apache httpd:
Start the web server. OMERO.web should now be reachable at
<http://<hostname>/webclient> (for the main client interface) and at
<http://<hostname>/webadmin> (for the administration interface).
omero web config apache-fcgi
Note that the OMERO web application does not seem to support being
published at any other place than the server root ("/"). If your
httpd server has another purposes beyong OMERO.web, you may want
to use a VirtualHost; in that case, include the OMERO.web
configuration inside a <VirtualHost> directive as follows:
---8<----------------------------------------------------------------
<VirtualHost server_ip:80>
ServerName server.hostname
...insert the above-mentioned configuration stanza...
</VirtualHost>
--->8----------------------------------------------------------------
Start the web server. OMERO.web should now be reachable at the root
of the web server.
6. BACKUP AND RESTORE
@ -198,7 +144,7 @@
http://www.openmicroscopy.org/site/support/omero5/sysadmins/server-upgrade.html
To upgrade OMERO 4.4.x to OMERO-5.0.x:
To upgrade OMERO 5.0.x to OMERO-5.1.x:
- stop OMERO if it is running;
@ -209,7 +155,7 @@
- upgrade the database:
$ cd /opt/omero
$ psql -h localhost -U omero omero < sql/psql/OMERO5.0__0/OMERO4.4__0.sql
$ psql -h localhost -U omero omero < sql/psql/OMERO5.1__1/OMERO5.0__0.sql
- start the upgraded server:

10
n/omero/omero.SlackBuild

@ -29,8 +29,8 @@
# Source package infos
NAMESRC=${NAMESRC:-OMERO.server}
VERSION=${VERSION:-5.0.8}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice35-b60.zip}
VERSION=${VERSION:-5.1.0}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice35-b40.zip}
WGET=${WGET:-http://downloads.openmicroscopy.org/omero/$VERSION/artifacts/$ARCHIVE}
# Build infos
@ -69,10 +69,9 @@ sha1sum -c $ARCHIVE.sha1
mkdir -p $PKG/opt
cd $PKG/opt
unzip $CWD/$ARCHIVE
mv OMERO.server-$VERSION-ice35-b60 omero
mv OMERO.server-$VERSION-ice35-b40 omero
rm omero/bin/*.bat
rm omero/etc/{Windows.cfg,apache.conf.template,env.bat,env.sh,local.properties.example}
rm omero/etc/nginx.conf.*
rm omero/etc/{Windows.cfg,env.bat,local.properties.example}
rm omero/etc/grid/windefault.xml
# Install launch scripts
@ -83,6 +82,7 @@ install -D -m 644 $CWD/rc.omero $PKG/etc/rc.d/rc.omero
mkdir -p $PKG/usr/doc/$NAMEPKG-$VERSION
install -m 644 $CWD/README $PKG/usr/doc/$NAMEPKG-$VERSION
mv omero/LICENSE.txt $PKG/usr/doc/$NAMEPKG-$VERSION
mv omero/history.txt $PKG/usr/doc/$NAMEPKG-$VERSION
mv omero/licenses $PKG/usr/doc/$NAMEPKG-$VERSION/licenses
# Copy slack-desc and doinst.sh files

3
n/omero/omero.sh

@ -1,7 +1,6 @@
#!/bin/sh
OMERO_HOME=/opt/omero
PYTHONPATH=/opt/omero/lib/python
export OMERO_HOME
export PYTHONPATH
exec $OMERO_HOME/bin/omero $@
exec /opt/omero/bin/omero $@

18
n/omero/rc.omero

@ -16,9 +16,17 @@ init)
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=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.name=(.*)$/\1/p')
DB_USER=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.user=(.*)$/\1/p')
DB_PASS=$(echo "$CONFIG" | sed -nre 's/^omero\.db\.pass=(.*)$/\1/p')
[ -n "$DATADIR" ] || DATADIR=/OMERO
[ -n "$DB_HOST" ] || DB_HOST=localhost
[ -n "$DB_PORT" ] || DB_PORT=5432
[ -n "$DB_NAME" ] || DB_NAME=omero
[ -n "$DB_USER" ] || DB_USER=omero
[ -n "$DB_PASS" ] || DB_PASS=omero
PGOPTS="-h $DB_HOST -p $DB_PORT -U $DB_ROOT"
if [ ! -d $DATADIR ]; then
@ -29,16 +37,16 @@ init)
if ! psql $PGOPTS -c '\du' | grep -q $DB_USER ; then
echo Creating database user...
createuser $PGOPTS -P -D -R -S $DB_USER
psql $PGOPTS -c "CREATE ROLE $DB_USER LOGIN WITH PASSWORD '$DB_PASS'"
fi
if ! psql $PGOPTS -l | grep -q $DB_NAME ; then
echo Creating database...
createdb $PGOPTS -O $DB_USER $DB_NAME
createdb $PGOPTS -E UTF8 -l en_US.UTF-8 -T template0 -O $DB_USER $DB_NAME
createlang $PGOPTS plpgsql $DB_NAME
sudo -H -u omero -i omero db script
psql -h $DB_HOST -p $DB_PORT -U $DB_USER $DB_NAME < /var/lib/omero/OMERO5.0__0.sql
rm -rf /var/lib/omero/OMERO5.0__0.sql
psql -h $DB_HOST -p $DB_PORT -U $DB_USER $DB_NAME < /var/lib/omero/OMERO5.1__1.sql
rm -rf /var/lib/omero/OMERO5.1__1.sql
fi
;;

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