Browse Source

n/omero-server: Upgraded to omero-server-5.6.0.

current-20191101
Damien Goutte-Gattat 2 years ago
parent
commit
95bad1ad95
  1. 1
      n/omero-server/OMERO.server-5.5.1-ice36-b122.zip.sha256
  2. 1
      n/omero-server/OMERO.server-5.6.0-ice36-b136.zip.sha256
  3. 28
      n/omero-server/README
  4. 1
      n/omero-server/omero-py-5.6.0.tar.gz.sha256
  5. 38
      n/omero-server/omero-server.SlackBuild
  6. 2
      n/omero-server/omero.sh
  7. 7
      n/omero-server/rc.omero

1
n/omero-server/OMERO.server-5.5.1-ice36-b122.zip.sha256

@ -1 +0,0 @@
e097ad45ebd275dfc4795b479ad4be36567a11d53be726e16325c159e814012c OMERO.server-5.5.1-ice36-b122.zip

1
n/omero-server/OMERO.server-5.6.0-ice36-b136.zip.sha256

@ -0,0 +1 @@
3a9f26637ee69d5f82f9ca9aa56fea9c890983c7557bdebfb8d0b1e8d720aa7b OMERO.server-5.6.0-ice36-b136.zip

28
n/omero-server/README

@ -1,4 +1,4 @@
PACKAGER'S README FOR OMERO-5.5.1
PACKAGER'S README FOR OMERO-5.6.0
Damien Goutte-Gattat <dgouttegattat@incenp.org>
@ -86,8 +86,8 @@
5. OMERO.web
The Django-based web application OMERO.web is not enabled by default,
as it requires some configuration.
The Django-based web application OMERO.web is no longer packaged
along with OMERO.server. Use the n/omero-web package to install it.
Make sure Nginx and Django are installed. Add the following line to
the OMERO configuration file /etc/omero.conf:
@ -96,23 +96,13 @@
omero.web.application_server=wsgi
--->8----------------------------------------------------------------
Then, edit the control script /etc/rc.d/rc.omero to automatically
start OMERO.web alongside the OMERO server itself:
---8<----------------------------------------------------------------
OMERO_WEB_ENABLED=yes
--->8----------------------------------------------------------------
Then, you need to install and configure the Apache HTTP server to
actually serve the application.
The following command will produce a configuration snippet that can
directly inserted into the configuration file of Nginx:
Then, use the following command to produce a configuration snippet
that can be directly inserted into the configuration of Nginx:
omero web config nginx
Start the web server. OMERO.web should now be reachable at the root
of the web server.
Start the web server, the OMERO server itself and the OMERO.web
workers using the rc scripts provided in the corresponding packages.
6. BACKUP AND RESTORE
@ -140,7 +130,9 @@
http://www.openmicroscopy.org/site/support/omero5/sysadmins/server-upgrade.html
To upgrade OMERO 5.4.x to OMERO-5.5.1:
To upgrade OMERO 5.5.x to OMERO-5.6.0:
- Make sure you have Python3, as OMERO-5.6.0 no longer supports Python2;
- stop OMERO if it is running;

1
n/omero-server/omero-py-5.6.0.tar.gz.sha256

@ -0,0 +1 @@
e75f53cd59a37db2f58699114a9c8306361732f27d392e5f25dcf267f583e8e7 omero-py-5.6.0.tar.gz

38
n/omero-server/omero-server.SlackBuild

@ -1,6 +1,6 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2009-2019 Damien Goutte-Gattat
# Copyright (C) 2009-2020 Damien Goutte-Gattat
#
# Redistribution and use of this script, with or without modifications,
# is permitted provided that the following conditions are met:
@ -24,12 +24,12 @@
#
# Latest omero sourcecode is available at: <http://www.openmicroscopy.org/>.
#
# Depends: d/ice, n/gunicorn, l/omero-marshal, l/django-pipeline, l/pytables
# Depends: l/ice-py, l/omero-marshal, l/pytables
# Source package infos
NAMESRC=${NAMESRC:-OMERO.server}
VERSION=${VERSION:-5.5.1}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice36-b122.zip}
VERSION=${VERSION:-5.6.0}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION-ice36-b136.zip}
WGET=${WGET:-http://downloads.openmicroscopy.org/omero/$VERSION/artifacts/$ARCHIVE}
# Build infos
@ -64,12 +64,18 @@ if [ ! -r $ARCHIVE ]; then
fi
sha256sum -c $ARCHIVE.sha256
# Get and verify OMERO.py
if [ ! -r omero-py-$VERSION.tar.gz ]; then
pip3 download --no-binary :all: --no-deps omero-py==$VERSION
fi
sha256sum -c omero-py-$VERSION.tar.gz.sha256
# Extract and install
mkdir -p $PKG/opt
cd $PKG/opt
unzip $CWD/$ARCHIVE
mv OMERO.server-$VERSION-ice36-b122 omero
rm omero/bin/*.bat omero/etc/env.bat
mv OMERO.server-$VERSION-ice36-b136 omero
rm omero/etc/env.bat
# Install launch scripts
install -D -m 755 $CWD/omero.sh $PKG/usr/bin/omero
@ -85,6 +91,21 @@ mv omero/LICENSE.txt $PKG/usr/doc/$NAMEPKG-$VERSION
mv omero/history.rst $PKG/usr/doc/$NAMEPKG-$VERSION
mv omero/share/licenses $PKG/usr/doc/$NAMEPKG-$VERSION/licenses
# Install OMERO.py
# This used to be provided along with OMERO.server, but is now
# distributed on PyPI. However given that OMERO.py is necessary
# to even start the server, I don't see the point of packaging
# it separately.
cd $TMP
tar xf $CWD/omero-py-$VERSION.tar.gz
cd omero-py-$VERSION
python3 setup.py build
python3 setup.py install \
--install-lib=/opt/omero/lib/python \
--install-scripts=/opt/omero/bin \
--root=$PKG
rm $PKG/opt/omero/bin/{omero,setpythonpath,winconfig}.bat
# Copy slack-desc and doinst.sh files
mkdir -p $PKG/install
install -m 644 $CWD/slack-desc $PKG/install/slack-desc
@ -92,9 +113,7 @@ install -m 755 $CWD/doinst.sh $PKG/install/doinst.sh
# Add dependency infos
cat <<EOF > $PKG/install/slack-required
django-pipeline
gunicorn
ice
ice-py
omero-marshal
pytables
EOF
@ -106,6 +125,7 @@ PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/omero-py-$VERSION
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot

2
n/omero-server/omero.sh

@ -1,5 +1,7 @@
#!/bin/sh
PYTHONPATH=/opt/omero/lib/python
OMERODIR=/opt/omero
export PYTHONPATH
export OMERODIR
exec /opt/omero/bin/omero $@

7
n/omero-server/rc.omero

@ -3,7 +3,6 @@
DB_ROOT=postgres
CONFIG_FILE=/etc/omero.conf
ICEGRID_PIDFILE=/opt/omero/var/master/master.pid
OMERO_WEB_ENABLED=no
case "$1" in
init)
@ -51,16 +50,10 @@ init)
start)
sudo -H -u omero -i omero admin start
if [ "x$OMERO_WEB_ENABLED" = xyes ]; then
sudo -H -u omero -i omero web start
fi
;;
stop)
if [ -f $ICEGRID_PIDFILE ] && kill -0 $(< $ICEGRID_PIDFILE) 2>/dev/null ; then
if [ "x$OMERO_WEB_ENABLED" = xyes ]; then
sudo -H -u omero -i omero web stop
fi
sudo -H -u omero -i omero admin stop
rm -f $ICEGRID_PIDFILE
fi

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