Merge pull request #141 from johanherman/jointcalling

Add PyVCF for joint calling

roles/ngi_pipeline/tasks/main.yml

@@ -32,6 +32,9 @@
 - name: Create ngi pipeline conf directory 
   file: path="{{ ngi_pipeline_conf }}" state=directory mode=g+s
 
+- name: Install PyVCF for joint calling 
+  shell: "{{ ngi_pipeline_venv }}/bin/pip install PyVCF"
+
 - name: Create ngi_resources folder 
   file: name={{ ngi_resources }} state=directory mode=g+s
 
@@ -83,9 +86,3 @@
               line='export PATH={{ anaconda_path }}/bin:$PATH'
               backup=no
 
-# Ugly fix for now for some easy_install files that loses their permission under anaconda
-# FIXME: Doesn't work when we are several people that have installed sw. 
-#- name: manually fix group permissions for anaconda 
-#  shell: "chmod -R g+rwX {{ anaconda_path }}"
-#  tags: ngi_pipeline 
-