Start work on Ubuntu 11.04; updated configuration, packages and docs

README.md

@@ -263,13 +263,19 @@ Allow ssh and web access to your instances:
 
 Each time you'd like to use EC2, you need to create a remote instance to work
 with, which can be done nicely via the [AWS console][4]. Pick an AMI,
-start an instance and ensure that it is running. You will
-need to increase the size of the root filesystem to fit all of the
-CloudBioLinux data and libraries. This is done by ssh-ing in to the
-machine:
+start an instance and ensure that it is running. 
+
+For building from scratch, you will need to increase the size of the 
+root filesystem to fit all of the CloudBioLinux data and libraries. 
+This is done by starting the instance from the commandline:
+
+       % ec2-run-instances ami-cef405a7 -k sobchak-keypair -t m1.large -b /dev/xvda1=:20
+       % ec2-describe-instances i-0ca39764
+
+Then ssh to the machine:
 
        % ssh -i ~/.ec2/id-sobchak.keypair ubuntut@ec2-174-129-68-135.compute-1.amazonaws.com
-       % sudo resize2fs /dev/sda1
+       % sudo resize2fs /dev/xvda1
        % df -h
 
 # LICENSE

config/fabricrc.txt

@@ -8,7 +8,7 @@
 # details about the operating system
 ## Ubuntu
 distribution = ubuntu
-dist_name = maverick
+dist_name = natty
 ## Centos
 #distribution = centos
 ## Debian

config/packages.yaml

@@ -284,9 +284,9 @@ bio_alignment:
   - probcons
   - t-coffee
   - bio-linux-seaview
-  - bio-linux-clustal
+  #- bio-linux-clustal
   - bio-linux-dotter
-  - bio-linux-jalview
+  #- bio-linux-jalview
   - bio-linux-pfaat
   - bio-linux-prank
   - bio-linux-squint
@@ -337,7 +337,7 @@ bio_utils:
   - bio-linux-base-directories
   - bio-linux-bldp-files
   - bio-linux-sampledata
-  - bio-linux-sequin
+  #- bio-linux-sequin
   - bio-linux-taxinspector
   - bio-linux-themes-v5
 phylogeny:
@@ -347,7 +347,7 @@ phylogeny:
     - mrbayes
     - njplot
     - tree-puzzle
-    - bio-linux-arb
+    #- bio-linux-arb
     - bio-linux-coalesce
     - bio-linux-dendroscope
     - bio-linux-fastDNAml

config/python-libs.yaml

@@ -21,6 +21,7 @@ pypi:
   - pyyaml
   - routes
   - simplejson
+  - sphinx
   - webhelpers
   - webob
   - xlrd

fabfile.py

@@ -132,8 +132,8 @@ def _setup_ubuntu():
       "deb-src http://us.archive.ubuntu.com/ubuntu/ %s-updates multiverse",
       "deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen", # mongodb
       "deb http://cran.stat.ucla.edu/bin/linux/ubuntu %s/", # lastest R versions
-      "deb http://archive.cloudera.com/debian %s-cdh3 contrib", # Hadoop
-      "ppa:sun-java-community-team/sun-java6", # sun-java
+      "deb http://archive.cloudera.com/debian maverick-cdh3 contrib", # Hadoop
+      "deb http://archive.canonical.com/ubuntu maverick partner", # sun-java
     ] + shared_sources
     env.std_sources = _add_source_versions(version, sources)