updated installation process

.travis.yml

@@ -4,17 +4,8 @@ language: python
 python:
   - "2.7"
 
-before_install:
-  - chmod +x setup-DEBs.sh
-  - sudo ./setup-DEBs.sh
-
-install:
-  - chmod +x setup-DEBs.sh
-  - sudo ./setup-CGAT.sh
-
 script: 
-  - chmod +x nosetests-DEBs.sh
-  - sudo ./nosetests-DEBs.sh
+  - sudo ./install-CGAT-tools.sh --travis
 
 notifications:
   email:

INSTALL

@@ -1,7 +1,17 @@
 REQUIREMENTS
 
+   # Become root and do:
+   ./install-CGAT-tools.sh --install-os-packages
+
 INSTALL
 
-    sh install_prerequisites.sh
-    python setup.py install
+    # As non-root user:
+   ./install-CGAT-tools.sh --install-python-deps
+
+NOTES
+
+    The "install-CGAT-tools.sh" script works only in Ubuntu 12.x and Scientific Linux 6.x
+
+    Please visit the following page to find more information about alternative installation methods:
+    http://www.cgat.org/~andreas/documentation/cgat/CGATInstallation.html
 

doc/CGATInstallationSL6.rst

@@ -23,23 +23,21 @@ Get a copy of the installation scripts
 Download and place them into your home directory::
 
         cd
-        wget https://raw.github.com/CGATOxford/cgat/master/requires.txt
-        wget https://raw.github.com/CGATOxford/cgat/master/setup-RPMs.sh
-        wget https://raw.github.com/CGATOxford/cgat/master/setup-CGAT.sh
+        wget https://raw.github.com/CGATOxford/cgat/master/install-CGAT-tools.sh
 
 Install RPM dependencies
 ------------------------
 
-Become root (or ask your system administrator to do it for you) and run ``setup-RPMs.sh``::
+Become root (or ask your system administrator to do it for you) and run::
 
-        ./setup-RPMs.sh
+        ./install-CGAT-tools.sh --install-os-packages
 
 Install a Python virtual environment with the CGAT code collection
 ------------------------------------------------------------------- 
 
-Do not be root for this step and run ``setup-CGAT.sh``::
+Do not be root for this step and run::
 
-        ./setup-CGAT.sh
+        ./install-CGAT-tools.sh --install-python-deps
 
 Test the installation
 ---------------------

doc/CGATInstallationUbuntu.rst

@@ -20,23 +20,21 @@ Get a copy of the installation scripts
 Download and place them into your home directory::
 
         cd
-        wget https://raw.github.com/CGATOxford/cgat/master/requires.txt
-        wget https://raw.github.com/CGATOxford/cgat/master/setup-DEBs.sh
-        wget https://raw.github.com/CGATOxford/cgat/master/setup-CGAT.sh
+        wget https://raw.github.com/CGATOxford/cgat/master/install-CGAT-tools.sh
 
 Install DEB dependencies
 ------------------------
 
-Become root (or ask your system administrator to do it for you) and run ``setup-DEBs.sh``::
+Become root (or ask your system administrator to do it for you) and run::
 
-        ./setup-DEBs.sh
+        ./install-CGAT-tools.sh --install-os-packages
 
 Install a Python virtual environment with the CGAT code collection
 ------------------------------------------------------------------- 
 
-Do not be root for this step and run ``setup-CGAT.sh``::
+Do not be root for this step and run::
 
-        ./setup-CGAT.sh
+        ./install-CGAT-tools.sh --install-python-deps
 
 Test the installation
 ---------------------