diff --git a/singularity/Singularity b/singularity/Singularity index ea57eab419d17c89af36e6d2040bf0a00b18d120..125f213248958bfcacee34766140fb6c2f8cc3ee 100644 --- a/singularity/Singularity +++ b/singularity/Singularity @@ -15,15 +15,7 @@ ln -sf /bin/bash /bin/sh # INSTALL SYSTEM DEPS ##################### -apt-get update -y && apt-get install -y python3-pip \ - python3-venv - - -# SET UP VIRTUALENV -################### -export VIRTUALENV_DIR="/usr/local/share/ost_venv" -python3 -m venv --system-site-packages $VIRTUALENV_DIR -. $VIRTUALENV_DIR/bin/activate +apt-get update -y && apt-get install -y python3-pip pip3 install nglview \ ipython \ jupyter @@ -71,7 +63,6 @@ export IPYTHONDIR="/usr/local/share/ipython" export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter" export JUPYTER_PATH="/usr/local/share/jupyter" export JUPYTER_RUNTIME_DIR="/usr/local/share/jupyter/runtime" -export VIRTUALENV_DIR="/usr/local/share/ost_venv" %apprun ChemdictTool @@ -181,7 +172,7 @@ export DNG_INITDIR=${DNG_ROOT}/lib64/python3.6/site-packages/ost ############################################################################## # OST IPYTON APP ############################################################################## -. $VIRTUALENV_DIR/bin/activate && ipython3 -i $DNG_INITDIR/ost_startup.py "$@" +ipython3 -i $DNG_INITDIR/ost_startup.py "$@" %apphelp IPython OST-powered iPython shell. @@ -208,7 +199,7 @@ export XDG_RUNTIME_DIR="" ############################################################################## # NOTEBOOK APP ############################################################################## -. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@" +jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@" %apphelp Notebook A Jupyter notebook playground with OST and nglview. @@ -235,8 +226,6 @@ For more details on how to use nglview see http://nglviewer.org/nglview/latest/. As the Singularity mounts $HOME by default Jupyter and Ipython config files are moved to separate directories. Proper environmental variables are also set. -In addition, Jupyter is run in a separate virtualenv to not interact with -possibly installed host version. To list of all available options: