Return to Question

I have a similar Ubuntu 14.04 VM working, would it be possible to rsync certain folders to it so that the non-working Ubuntu 14.04 is back to normal?

The contents of $PYTHONPATH before doing any source'ing are empty.

The contents of Downloads/dx-toolkit/environment are below:

# -*- Mode: shell-script -*-                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
# Copyright (C) 2013-2016 DNAnexus, Inc.                                                                                                                                                                                                                                                                                                                                                                                                                                                       
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
# This file is part of dx-toolkit (DNAnexus platform client libraries).                                                                                                                                                                                                                                                                                                                                                                                                                        
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#   Licensed under the Apache License, Version 2.0 (the "License"); you may not                                                                                                                                                                                                                                                                                                                                                                                                                
#   use this file except in compliance with the License. You may obtain a copy                                                                                                                                                                                                                                                                                                                                                                                                                 
#   of the License at                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#       http://www.apache.org/licenses/LICENSE-2.0                                                                                                                                                                                                                                                                                                                                                                                                                                             
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#   Unless required by applicable law or agreed to in writing, software                                                                                                                                                                                                                                                                                                                                                                                                                        
#   distributed under the License is distributed on an "AS IS" BASIS, WITHOUT                                                                                                                                                                                                                                                                                                                                                                                                                  
#   WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the                                                                                                                                                                                                                                                                                                                                                                                                                   
#   License for the specific language governing permissions and limitations                                                                                                                                                                                                                                                                                                                                                                                                                    
#   under the License.                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
# Source this file in a bash shell to initialize DNAnexus environment                                                                                                                                                                                                                                                                                                                                                                                                                          
# variables:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
# $ source environment                                                                                                                                                                                                                                                                                                                                                                                                                                                                         

# This line is compatible with both bash and csh/tcsh. If running in csh, it sources the file "environment.csh" and quits.                                                                                                                                                                                                                                                                                                                                                                     

test ! -z "$version" && echo "$shell" | grep -q csh && set SOURCE=`echo $_ | cut -f 2 -d " "` && set SOURCE=`dirname "$SOURCE"` && source "$SOURCE/environment.csh" && exit

# Resolve the location of this file                                                                                                                                                                                                                                                                                                                                                                                                                                                            
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ] ; do SOURCE="$(readlink "$SOURCE")"; done

# Get RHEL version                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
if [ -e /etc/redhat-release ] ; then
  RHEL_MAJOR_VERSION=$(grep -o "Red Hat Enterprise Linux .* release [0-9]\+" /etc/redhat-release | sed -e "s/Red Hat Enterprise Linux .* release //")
fi

export DNANEXUS_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

# Detect system installation of dx-toolkit                                                                                                                                                                                                                                                                                                                                                                                                                                                     
if [ "$DNANEXUS_HOME" == "/etc/profile.d" ]; then

  export DNANEXUS_HOME="/usr/share/dnanexus"
  # Private Python packages. We really ought not pollute PYTHONPATH with these though.                                                                                                                                                                                                                                                                                                                                                                                                         
  export PYTHONPATH="/usr/share/dnanexus/lib/python2.7/site-packages:$PYTHONPATH"
  export CLASSPATH="/usr/share/java/dnanexus-api-0.1.0.jar:${CLASSPATH}"

else

  export PATH="${DNANEXUS_HOME}/bin:$PATH"
  export CLASSPATH="${DNANEXUS_HOME}/lib/java/*:${CLASSPATH}"

  if [ "$RHEL_MAJOR_VERSION" == "7" ]; then
    export PYTHONPATH="${DNANEXUS_HOME}/share/dnanexus/lib/python2.7/site-packages:${DNANEXUS_HOME}/lib64/python2.7/site-packages:$PYTHONPATH"
  else
    export PYTHONPATH="${DNANEXUS_HOME}/share/dnanexus/lib/python2.7/site-packages:${DNANEXUS_HOME}/lib/python:$PYTHONPATH"
  fi

fi

# Note: The default I/O stream encoding in Python 2.7 (as configured on ubuntu) is ascii, not UTF-8 or the system locale                                                                                                                                                                                                                                                                                                                                                                       
# encoding. We reset it here to avoid having to set it for every I/O operation explicitly.                                                                                                                                                                                                                                                                                                                                                                                                     
export PYTHONIOENCODING=UTF-8

eval "$(register-python-argcomplete dx|sed 's/-o default//')"

# Clean up old session files                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
(shopt -s nullglob;
 if [[ $HOME != "" ]]; then
     for session_dir in "${HOME}/.dnanexus_config/sessions/"*; do
         if ! ps -p $(basename "$session_dir") &> /dev/null; then
             rm -rf "$session_dir"
         fi
     done
 fi
)

if [[ -z "$DX_SECURITY_CONTEXT" && -n "$DX_AUTH_TOKEN" ]]; then
    export DX_SECURITY_CONTEXT="{\"auth_token_type\":\"Bearer\",\"auth_token\":\"$DX_AUTH_TOKEN\"}"
fi

After doing unset PYTHON, then:

>>> import sys
>>> sys.path
['', '/usr/local/lib/python2.7/dist-packages/multiqc-1.4dev-py2.7.egg', '/usr/lib/python2.7/dist-packages', '/usr/lib/pymodules/python2.7', '/home/avilella/Downloads/dx-toolkit/share/dnanexus/lib/python2.7/site-packages', '/home/avilella/Downloads/dx-toolkit/lib/python', '/home/avilella', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/home/avilella/.local/lib/python2.7/site-packages', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/python2.7/dist-packages/ubuntu-sso-client']

unset PYTHON, the python3:

>>> import sys
>>> sys.path
['', '/home/avilella/Downloads/dx-toolkit/share/dnanexus/lib/python2.7/site-packages', '/home/avilella/Downloads/dx-toolkit/lib/python', '/home/avilella', '/usr/lib/python3.4', '/usr/lib/python3.4/plat-x86_64-linux-gnu', '/usr/lib/python3.4/lib-dynload', '/usr/local/lib/python3.4/dist-packages', '/usr/lib/python3/dist-packages']