From 84430c065baf40ee46b72c210fc96c9f3add565d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 16 Dec 2019 14:09:45 +0100
Subject: [PATCH] don't use virtualenv to make container simpler
---
singularity/Singularity | 17 +++--------------
1 file changed, 3 insertions(+), 14 deletions(-)
diff --git a/singularity/Singularity b/singularity/Singularity
index ea57eab41..125f21324 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:
--
GitLab