diff --git a/.omero/cli-build b/.omero/cli-build index c1e815e..ed09e48 100644 --- a/.omero/cli-build +++ b/.omero/cli-build @@ -11,6 +11,15 @@ cd $TARGET GUESS=${PWD#*omero-cli-*} PLUGIN=${PLUGIN:-$GUESS} +export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::") +export JAVA_LD_LIBRARY_PATH="$JAVA_HOME/lib/:$JAVA_HOME/lib/server" +export CONDA_BACKUP_JAVA_HOME=$JAVA_HOME +export CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH + +source /tmp/miniconda/bin/activate +conda init +conda activate omero + export OMERO_DIST=${OMERO_DIST:-/opt/omero/server/OMERO.server} omero $PLUGIN -h python setup.py test -t test -i ${OMERO_DIST}/etc/ice.config -vs diff --git a/.omero/py-setup b/.omero/py-setup index 590d731..2de7514 100644 --- a/.omero/py-setup +++ b/.omero/py-setup @@ -8,9 +8,18 @@ set -x TARGET=${TARGET:-..} PLUGIN=${PLUGIN:-} -python --version +export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::") +export JAVA_LD_LIBRARY_PATH="$JAVA_HOME/lib/:$JAVA_HOME/lib/server" +export CONDA_BACKUP_JAVA_HOME=$JAVA_HOME +export CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH +wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +sh Miniconda3-latest-Linux-x86_64.sh -b -p /tmp/miniconda +source /tmp/miniconda/bin/activate +conda init +conda create -n omero python=3.8 +conda activate omero pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20231130/zeroc_ice-3.6.5-cp39-cp39-manylinux_2_28_x86_64.whl -pip install bftools +conda install -c bioconda bftools cd $TARGET cd $(setup_dir)