Only add python-software-properties if needed; correct distribution r…

…ewrites for BioNode

cloudbio/distribution.py

@@ -45,7 +45,6 @@ def _setup_ubuntu():
     env.logger.info("Ubuntu setup")
     shared_sources = _setup_deb_general()
     # package information. This is ubuntu/debian based and could be generalized.
-    version = env.dist_name
     sources = [
       "deb http://us.archive.ubuntu.com/ubuntu/ %s universe", # unsupported repos
       "deb http://us.archive.ubuntu.com/ubuntu/ %s multiverse",
@@ -58,19 +57,18 @@ def _setup_ubuntu():
       "deb http://archive.canonical.com/ubuntu maverick partner", # sun-java
       "deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu lucid main", # Free-NX
     ] + shared_sources
-    env.std_sources = _add_source_versions(version, sources)
+    env.std_sources = _add_source_versions(env.dist_name, sources)
 
 def _setup_debian():
     env.logger.info("Debian setup")
     shared_sources = _setup_deb_general()
-    version = env.dist_name
     sources = [
         "deb http://downloads-distro.mongodb.org/repo/debian-sysvinit dist 10gen", # mongodb
         "deb http://cran.stat.ucla.edu/bin/linux/debian %s-cran/", # latest R versions
         "deb http://archive.cloudera.com/debian lenny-cdh3 contrib" # Hadoop
         ] + shared_sources
     # fill in %s
-    env.std_sources = _add_source_versions(version, sources)
+    env.std_sources = _add_source_versions(env.dist_name, sources)
 
 def _setup_deb_general():
     """Shared settings for different debian based/derived distributions.

cloudbio/edition/base.py

@@ -71,8 +71,10 @@ def rewrite_apt_sources_list(self, sources):
             main_repository = 'http://ftp.us.debian.org/debian/'
         else:
             main_repository = env.debian_repository
-        new_sources = ["deb {repo} %s main contrib non-free".format(repo=main_repository),
-                       "deb {repo} %s-updates main contrib non-free".format(repo=main_repository)]
+        new_sources = ["deb {repo} {dist} main contrib non-free".format(repo=main_repository,
+                                                                        dist=env.dist_name),
+                       "deb {repo} {dist}-updates main contrib non-free".format(
+                           repo=main_repository, dist=env.dist_name)]
         return sources + new_sources
 
 class Minimal(Edition):

config/packages.yaml

@@ -101,6 +101,7 @@ programming:
     - gfortran
     - stow
     - rsync
+    - python-software-properties
   libraries:
     - libatlas-base-dev
     - libatlas-dev

fabfile.py

@@ -484,7 +484,6 @@ def _setup_apt_sources():
 
        Uses python-software-properties, which provides an abstraction of apt repositories
     """
-    sudo("apt-get install -y --force-yes python-software-properties")
     env.edition.check_packages_source()
 
     comment = "# This file was modified for "+ env.edition.name
@@ -495,6 +494,7 @@ def _setup_apt_sources():
     for source in env.edition.rewrite_apt_sources_list(env.std_sources):
         env.logger.debug("Source %s" % source)
         if source.startswith("ppa:"):
+            sudo("apt-get install -y --force-yes python-software-properties")
             sudo("add-apt-repository '%s'" % source)
         elif not contains(env.sources_file, source):
             append(env.sources_file, source, use_sudo=True)