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Update Bio-Linux packages to 12.04. Update repository links. Thanks to

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1 parent d6aaaab commit a1781a36a601b54d7165ce76d4a5ee2b4f670a4b @chapmanb committed
Showing with 42 additions and 49 deletions.
  1. +2 −1 cloudbio/distribution.py
  2. +1 −1 cloudbio/edition/base.py
  3. +39 −47 config/packages.yaml
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3 cloudbio/distribution.py
@@ -81,6 +81,7 @@ def _setup_ubuntu():
"deb http://archive.cloudera.com/debian maverick-cdh3 contrib", # Hadoop
"deb http://archive.canonical.com/ubuntu %s partner", # sun-java
"deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu %s main", # Free-NX
+ "deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu %s main", # Free-NX
] + shared_sources
env.std_sources = _add_source_versions(env.dist_name, sources)
@@ -108,7 +109,7 @@ def _setup_deb_general():
# XXX look for a way to find JAVA_HOME automatically
env.java_home = "/usr/lib/jvm/java-6-openjdk"
shared_sources = [
- "deb http://nebc.nox.ac.uk/bio-linux/ unstable bio-linux", # Bio-Linux
+ "deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux", # Bio-Linux
"deb http://download.virtualbox.org/virtualbox/debian %s contrib"
]
return shared_sources
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2 cloudbio/edition/base.py
@@ -118,7 +118,7 @@ def rewrite_apt_sources_list(self, sources):
"deb {repo} testing main contrib non-free".format(
repo=main_repository)
]
- new_sources = new_sources + [ "deb http://nebc.nox.ac.uk/bio-linux/ unstable bio-linux" ]
+ new_sources = new_sources + [ "deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux" ]
return new_sources
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86 config/packages.yaml
@@ -47,7 +47,6 @@ minimal:
- openssh-server
- screen
- unzip
- - tar
- less
network:
- curl
@@ -112,7 +111,6 @@ programming:
- libncurses5-dev
- zlib1g-dev
- libssl-dev
- - libpcre3
- libpcre3-dev
- libreadline-dev
- mime-support
@@ -191,7 +189,6 @@ distributed:
- hadoop-0.20-pipes
- hadoop-0.20-source
- libopenmpi-dev
- - libopenmpi1.3
- openmpi-bin
- libzmq-dev
- libfuse-dev
@@ -228,7 +225,6 @@ r:
- r-base-dev
- r-base-html
perl:
- - perl-base
- perl
- libperl-dev
- perl-modules
@@ -317,93 +313,96 @@ boinc:
- boinc-manager
bio_general:
- primer3
- - readseq
- - bio-linux-xcut
+ - bio-linux-catchall
+ - bio-linux-emboss
+ - bio-linux-readseq
- emboss
- emboss-data
- emboss-lib
- jemboss
- ugene
- # - bio-linux-taverna # Broken graphviz dependency
bio_search:
- blast2
- - hmmer
- ncbi-tools-bin
- - bio-linux-blast+
+ - bio-linux-blast
- bio-linux-blixem
- bio-linux-fasta
+ - bio-linux-hmmer
- bio-linux-mspcrunch
- bio-linux-mview
- bio-linux-nrdb
+ - cdbfasta
bio_alignment:
- - clustalw
+ - bio-linux-clustal
+ - bio-linux-dotter
+ - bio-linux-jalview
+ - bio-linux-mcl
+ - bio-linux-mummer
+ - bio-linux-pfaat
+ - bio-linux-seaview
+ - bio-linux-squint
+ - bio-linux-t-coffee
- exonerate
- mafft
- muscle
- - mummer
+ - prank
- probcons
- - t-coffee
- - bio-linux-seaview
- - bio-linux-clustal # Version problem
- - bio-linux-dotter
- - bio-linux-jalview # Version problem
- - bio-linux-pfaat
- - bio-linux-prank
- - bio-linux-squint
- - bio-linux-wise2
+ - wise
bio_nextgen:
+ - bio-linux-fastqc
- fastx-toolkit
- maq
- plink
- last-align
- tabix
- # - samtools # very old version
+ - samtools # now up-to-date again
bio_sequencing:
- bio-linux-assembly-conversion-tools
- bio-linux-cap3
- bio-linux-dust
- bio-linux-lucy
+ - bio-linux-mira
+ - bio-linux-mira-3rd-party
- bio-linux-staden
- bio-linux-stars
- # Install problems with emboss: - bio-linux-msatfinder
- #- bio-linux-mira # need mira-assembler but gone from repo
- #- bio-linux-mira-3rd-party
+ - bio-linux-tablet
bio_annotation:
- mcl
+ - predictprotein
- tigr-glimmer
- bio-linux-artemis
- bio-linux-big-blast
- bio-linux-cd-hit
- bio-linux-estscan
- bio-linux-glimmer3
- - bio-linux-partigene
- - bio-linux-prot4est
+ - bio-linux-jprofilegrid
+ - bio-linux-msatfinder
+# - bio-linux-prot4est - broken, fix in progress
- bio-linux-rbs-finder
- bio-linux-transterm-hp
- bio-linux-trnascan
- bio-linux-tetra
- # Conflict: - bio-linux-act
# 500Mb of disk: - bio-linux-priam
- # Package broken: - bio-linux-yamap
+bio_markergenes:
+ - bio-linux-ampliconnoise
+ - bio-linux-jmotu
+ - bio-linux-mothur
+ - bio-linux-rdp-classifier
+ - bio-linux-qiime
bio_microarray:
- bio-linux-ocount
- bio-linux-oligoarray
- bio-linux-oligoarrayaux
bio_visualization:
- rasmol
- - bio-linux-clcsequenceviewer
- - bio-linux-maxd
+ # - bio-linux-clcsequenceviewer # Awaiting fix
bio_utils:
- - bio-linux-das-prep
- - bio-linux-exchanger
- bio-linux-genquery
- bio-linux-keyring
- - bio-linux-base-directories
- bio-linux-bldp-files
- bio-linux-sampledata
- - bio-linux-sequin # Version problem
- bio-linux-taxinspector
- - bio-linux-themes-v5
+ - bio-linux-xcut
phylogeny_testing:
# new packages in testing (Debian 'wheezy')
all:
@@ -422,25 +421,18 @@ phylogeny:
- njplot
- tree-puzzle
- bio-linux-arb
- # biolinux-ape package is source (i386). It needs R - not in deps - and
- # /usr/local/bioinf/ape# R CMD INSTALL ape (FIXME)
- # - bio-linux-ape
- - bio-linux-coalesce
+ - bio-linux-archaeopteryx
+ - bio-linux-cytoscape
- bio-linux-dendroscope
- - bio-linux-fastDNAml # Version problem
- - bio-linux-fluctuate
- - bio-linux-forester
+ - bio-linux-fastdnaml
- bio-linux-happy
- bio-linux-mesquite
- - bio-linux-migrate
- - bio-linux-mrbayes-multi
- #- bio-linux-mothur
+ - bio-linux-mrbayes
- bio-linux-paml
- bio-linux-omegamap
- bio-linux-qtlcart
- - bio-linux-recombine
- bio-linux-splitstree
- - bio-linux-treeview # Version problem
+ - bio-linux-treeview
needs_64bit:
- bio-linux-fasttree
## Package lists imported from mi-deployment.

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