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Small package fixes for ubuntu 12.04 builds

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1 parent da48edc commit 6d6f3900360d4e80eef8ceeaa5888356b7269209 @chapmanb chapmanb committed Jun 18, 2012
Showing with 8 additions and 10 deletions.
  1. +3 −3 cloudbio/custom/bio_nextgen.py
  2. +2 −2 cloudbio/distribution.py
  3. +1 −1 config/fabricrc.txt
  4. +1 −3 config/packages.yaml
  5. +1 −1 config/python-libs.yaml
@@ -301,14 +301,14 @@ def install_picard(env):
_java_install("picard", version, url, env)
def install_gatk(env):
- version = "1.6-5-g557da77"
+ version = "1.6-11-g3b2fab9"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
"GenomeAnalysisTK-%s%s" % (version, ext)
_java_install("gatk", version, url, env)
def install_gatk_queue(env):
- version = "1.5-12-gd0056d6"
+ version = "1.6-11-g3b2fab9"
ext = ".tar.bz2"
url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/"\
"Queue-%s%s" % (version, ext)
@@ -377,7 +377,7 @@ def _boost_build(env):
_get_install(url, env, _boost_build)
thread_lib = "libboost_thread.so.%s" % version
final_lib = os.path.join(env.system_install, "lib", thread_lib)
- orig_lib = os.pth.join(boost_dir, "lib", thread_lib)
+ orig_lib = os.path.join(boost_dir, "lib", thread_lib)
if not exists(final_lib):
env.safe_sudo("ln -s %s %s" % (orig_lib, final_lib))
View
@@ -79,8 +79,8 @@ def _setup_ubuntu():
"deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen", # mongodb
"deb http://watson.nci.nih.gov/cran_mirror/bin/linux/ubuntu %s/", # lastest R versions
"deb http://archive.cloudera.com/debian maverick-cdh3 contrib", # Hadoop
- "deb http://archive.canonical.com/ubuntu maverick partner", # sun-java
- "deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu lucid main", # Free-NX
+ "deb http://archive.canonical.com/ubuntu %s partner", # sun-java
+ "deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu %s main", # Free-NX
] + shared_sources
env.std_sources = _add_source_versions(env.dist_name, sources)
View
@@ -8,7 +8,7 @@
# details about the operating system
## Ubuntu
distribution = ubuntu
-dist_name = oneiric
+dist_name = precise
## Centos
#distribution = centos
## Debian
View
@@ -60,7 +60,6 @@ desktop:
- synaptic
- software-center
- freenx-server
- - gnome-themes
- gnome-backgrounds
- gnome-terminal
- firefox
@@ -188,7 +187,6 @@ distributed:
- hadoop-pig
- hadoop-hive
- libhdfs0-dev
- - hadoop-0.20-native
- hadoop-0.20-pipes
- hadoop-0.20-source
- libopenmpi-dev
@@ -319,12 +317,12 @@ boinc:
bio_general:
- primer3
- readseq
- - bio-linux-taverna
- bio-linux-xcut
- emboss
- emboss-data
- emboss-lib
- ugene
+ # - bio-linux-taverna # Broken graphviz dependency
bio_search:
- blast2
- hmmer
View
@@ -52,7 +52,6 @@ pypi:
- scikits.learn
- scikits.statsmodels
- scipy
- - sympy
# databases
- CouchDB
- h5py
@@ -72,3 +71,4 @@ pypi:
#- tables
#- pygraphviz
#- pysparse
+ #- sympy

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