Updated installation

.travis.yml

@@ -1,19 +1,38 @@
 
+# https://docs.travis-ci.com/user/multi-os/
+os:
+  - osx
+  - linux
+
 # use container-based infrastructure on Travis
 # http://docs.travis-ci.com/user/workers/container-based-infrastructure/
 # http://blog.travis-ci.com/2014-12-17-faster-builds-with-container-based-infrastructure/
-sudo: false
+#sudo: false
+
+# use VM infrastructure on Travis
+# exit code 137 indicates that your build is now taking more memory
+# or rather it's running alongside other builds requiring a lot of memory.
+# This can happen because your builds are running on container-based infrastructure and they will share the host's 4 GB memory.
+# To mitigate this situation, run your builds on our sudo-enabled Precise infrastructure.
+# Over there, your builds will run on a fully independent VM with 7.5 GB of (unshared) memory.
+sudo: required
+
+# http://mailchi.mp/travis-ci/ubuntu-trusty-update-2017q4-and-new-ltslatest-process?e=073d892e7f
+group: edge
 
-language: python
+language: generic
 
 env:
-  global:
-    - TEST_ALL=1
+  - TEST_ALL=1
 
-python:
-#  - "2.7"
-  - "3.5"
+# Using xvfb to Run Tests That Require a GUI
+# NOTE: The "before_script" section below does not work properly, but right now is not required
+# Linux: https://docs.travis-ci.com/user/gui-and-headless-browsers/#Using-xvfb-to-Run-Tests-That-Require-a-GUI
+#  OS X:https://github.com/travis-ci/travis-ci/issues/7313#issuecomment-279914149
+before_script:
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export DISPLAY=:99.0 && sh -e /etc/init.d/xvfb start && sleep 3 ; fi 
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ( sudo Xvfb :99 -ac -screen 0 1024x768x8 && echo ok )& ; fi
 
 script: 
-  - ./install-CGAT-tools.sh --travis
+  - travis_wait 30 ./install-CGAT-tools.sh --travis
 

CGATPipelines/PipelineMapping.py

@@ -2149,9 +2149,6 @@ def mapper(self, infiles, outfile):
 
         executable = self.executable
 
-        statement = P.getCondaEnvironment(PARAMS['conda_py2'])
-        statement.append(" && ")
-
         num_files = [len(x) for x in infiles]
 
         if max(num_files) != min(num_files):
@@ -2398,9 +2395,6 @@ def mapper(self, infiles, outfile):
 
         data_options = " ".join(data_options)
 
-        statement = P.getCondaEnvironment(PARAMS['conda_py2'])
-        statement.append(" && ")
-
         if nfiles == 1:
             infiles = ",".join([x[0] for x in infiles])
             statement.append('''