Add environment scripts to remove dx python2 from PYTHONPATH

wscleaner/README.md

@@ -52,6 +52,10 @@ optional arguments:
 pytest . --auth_token DNA_NEXUS_KEY
 ```
 
+## Workstation Environment
+The directory `env/` in this repository contains conda environment scripts for the workstation. These remove conflicts in the PYTHONPATH environment variable by editing the variable when conda is activated. The conda documentation describes where to place these scripts under ['saving environment variables'](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#macos-and-linux).
+
+
 ## License
 
 Developed by Viapath Genome Informatics

wscleaner/env/activate_env_vars.sh

@@ -0,0 +1,10 @@
+#!/bin/sh
+
+# Cache the python path
+export wsc_PPCACHE=$PYTHONPATH
+
+# Remove the dxtoolkit path from the pythonpath environment variable
+# Python searches this when importing modules, causing clashes with conda install 
+PYTHONPATH_CLEAN=$(echo $PYTHONPATH | sed s,/usr/share/dnanexus/lib/python2.7/site-packages:,,)
+# Set the new pythonpath
+export PYTHONPATH=$PYTHONPATH_CLEAN

wscleaner/env/deactivate_env_vars.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+# Set the python path to the original before the environment was active
+export PYTHONPATH=${wsc_PPCACHE}