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---
# List of packages to be installed via the package manager.
#
# This is derived from the Infochimps machetEC2 package:
#
# http://github.com/infochimps/machetec2
#
# and merged with packages from bioperl-max:
#
# http://fortinbras.us/bioperl-max/
#
# and biolinux:
#
# http://www.jcvi.org/cms/research/projects/jcvi-cloud-biolinux/included-software/
#
# Package names are the terminal symbols in the tree (the text on any
# line which begins with whitespace followed by a hypen and a space).
#
# The package list is organized taxonomically so that parts of it can
# be selectively installed/ignored. See main.yaml for top level configuration.
minimal:
#Packages to support a minimal installation (no X!)
administration:
- sudo
- htop
editors:
- vim
# don't put in emacs, as it pulls in X
version_control:
- git-core
- cvs
- subversion
- mercurial
- bzr
#- darcs # pulls in postfix mail configuration.
build:
- bsdmainutils
- clang
- cmake
- gcc
- g++
- gfortran
- libtool
- make
- patch
- pkg-config
util:
- axel
- gawk
- openssh-server
- pigz
- rsync
- screen
- unzip
- less
network:
- curl
- wget
libraries:
- libatlas-base-dev
#- libatlas-dev
- libblas-dev
- liblapack-dev
- libeigen3-dev
- libc6-dev
- libzip-dev
- libbz2-dev
- zlib1g-dev
- libcurl4-openssl-dev
- libgsl0-dev
- libgsl0ldbl
- gsl-bin
- mime-support
- libncurses5-dev
- libpcre3-dev
- libpng12-dev
- libreadline-dev
- libssl-dev
- uuid
- uuid-dev
- libxml2
- libxml2-dev
- libxslt1-dev
- libxslt1.1
- xz-utils
- liblzma-dev
- zlib1g-dev
- libnetcdf-dev
documentation:
- texlive-latex-base
- texlive-latex-recommended
- texlive-latex-extra
desktop:
#Packages to support a remote desktop
all:
- gnome-panel
- gnome-system-tools
- synaptic
- software-center
#- freenx-server # Gone on 14.04
- gnome-backgrounds
- gnome-terminal
- firefox
- evince
- ubuntu-desktop
- cloudbl-desktop
- bio-linux-tutorials
- xvfb
- gdm
# NX compatible window managers on Ubuntu 11.10+
ubuntu_oneiric:
- gnome-session-fallback
- unity-2d
ubuntu_lucid:
- rubygems
desktop-cloud:
# some special purpose VMs, such as BOINC, only require a minimal desktop
- lxde
- vnc4server
programming:
editors:
- emacs
- emacs-goodies-el
- emacsen-common
- exuberant-ctags
- gedit
build:
- libgtk2.0-dev
- protobuf-compiler
- python-software-properties
- stow
- swig
- rsync
- xfsprogs
filesystem:
- libfuse-dev
libraries:
- tcl-dev
- tk-dev
- imagemagick
- pdfjam
- libsparsehash-dev
- xvfb
- libboost-dev
- libboost-python-dev
- libboost-thread-dev
- libgd2-xpm-dev
- libgnomecanvas2-0
- libgnomecanvas2-dev
- libgnomevfs2-0
- libgnomevfs2-dev
- libgnomeui-0
- libgnomeui-dev
- libpango1.0-0
- libpango1.0-dev
- libx11-dev
packaging:
- build-essential
- devscripts
- debhelper
- dh-make
- pbuilder
- unzip
virtual:
#- virtualbox-4.2
- dkms
util:
- mc
- tree
- screen
- time
- fdupes
network:
- lynx
- traceroute
lang:
- aspell
- dictionaries-common
- libaspell-dev
distributed:
all:
- rabbitmq-server
- nfs-kernel-server
- nfs-common
- libopenmpi-dev
- openmpi-bin
- libzmq-dev
- libfuse-dev
# only for oneiric 11.10
ubuntu_oneiric:
- libmpich2-3
- libmpich2-dev
- mpich2
amazon:
- s3cmd
- euca2ools
python:
- python
- python-dev
- python-distutils-extra
- python-pip
- python-setuptools
- python-virtualenv
- python3
- python3-dev
- python-rpy
ruby:
- ruby1.9.1 # default Ruby install
- ruby1.9.1-dev
r:
- r-base
- r-base-core
- r-base-dev
- r-base-html
perl:
- perl
- libperl-dev
- perl-modules
- perl-tk
- parrot
- parrot-devel
- cpanminus
- libextutils-autoinstall-perl
java:
# - sun-java6-bin # Sun Java removed from Ubuntu package repositories
# - sun-java6-jre # Package 'sun-java6-jre' has no installation candidate
# - sun-java6-jdk Package 'sun-java6-jdk' has no installation candidate
- openjdk-7-jdk
- openjdk-7-jre
java_extras:
- openjdk-6-jdk
- openjdk-6-jre
- ant
- libbiojava-java
- libbiojava-java-demos
#- eclipse
- maven2
- libjline-java
- libjhdf5-java
- jruby
- jython
- scala
- scala-library
erlang:
- erlang
- erlang-base
- erlang-dev
- erlang-examples
- erlang-manpages
- erlang-mode
haskell:
- ghc
- cabal-install
- c2hs
databases:
mysql:
- mysql-client
- mysql-common
- mysql-server
- libmysqlclient15-dev
postgres:
- postgresql
- postgresql-client
- postgresql-plpython-9.3
- postgresql-plperl-9.3
- libpq-dev
sqlite:
- libsqlite0
- libsqlite0-dev
- libsqlite3-0
- libsqlite3-dev
- sqlite3
document:
- libdb-dev
- mongodb
- couchdb
- tokyocabinet-bin
- libtokyocabinet-dev
hdf:
- libhdf5-serial-dev
math:
- prover9
- octave
viz:
- imagemagick
- x11-apps
- mayavi2
- mtasc # for modest maps
- gnuplot
- graphviz
- libgraphviz-dev
- libgl1-mesa-dev
- libgl1-mesa-dri
- libgl1-mesa-glx
- libglu1-mesa
- libglu1-mesa-dev
web:
- apache2
boinc:
- boinc-client
- boinc-manager
bio_general:
- primer3
- bio-linux-catchall
# - bio-linux-emboss
- bio-linux-readseq
# - emboss # Broken on 13.10
# - emboss-data # Broken on 13.10
# - emboss-lib # broken on 13.10
# - jemboss # Broken on 13.10
- ugene
bio_search:
- blast2
- ncbi-tools-bin
- bio-linux-blast
- bio-linux-blixem
- bio-linux-fasta
- bio-linux-hmmer
- bio-linux-mspcrunch
- bio-linux-mview
# - bio-linux-nrdb # broken Depends: ia32-libs
- cdbfasta
bio_alignment:
# - bio-linux-clustal # Broken on 14.04
- bio-linux-dotter
#- bio-linux-jalview # Broken on 14.04
- bio-linux-mcl
- bio-linux-mummer
- bio-linux-pfaat
#- bio-linux-seaview # Broken on 14.04
- bio-linux-squint
- bio-linux-t-coffee
- exonerate
- mafft
- muscle
- bio-linux-prank
- probcons
- wise
bio_nextgen:
# - bio-linux-fastqc # out of date with brew latest
- fastx-toolkit
- maq
- plink
- last-align
- tabix
# - samtools # only on 0.18, prefer custom build
bio_sequencing:
#- bio-linux-assembly-conversion-tools # broken Depends: bio-linux-staden
- bio-linux-cap3
#- bio-linux-dust # broken on 14.04
#- bio-linux-lucy # broken on 14.04
# - bio-linux-staden # broken Depends: ia32-libs
# - bio-linux-stars # broken Depends: bio-linux-staden
- bio-linux-tablet
# - mira-assembler # broken on ubuntu 13.04
bio_annotation:
- mcl
- predictprotein
- tigr-glimmer
- bio-linux-artemis
- bio-linux-big-blast
- bio-linux-cd-hit
# - bio-linux-estscan # broken on ubuntu 14.04 (#163)
# - bio-linux-jprofilegrid # broken on 14.04
# - bio-linux-msatfinder # broken on 13.10
# - bio-linux-prot4est - broken, fix in progress
- bio-linux-rbs-finder
- bio-linux-transterm-hp
# - bio-linux-trnascan # Broken on 14.04
# - bio-linux-tetra # broken Depends: ia32-libs
# 500Mb of disk: - bio-linux-priam
bio_markergenes:
- bio-linux-ampliconnoise
- bio-linux-jmotu
- bio-linux-mothur
- bio-linux-rdp-classifier
- bio-linux-qiime
bio_microarray:
#- bio-linux-ocount # broken Depends: ia32-libs
- bio-linux-oligoarray
- bio-linux-oligoarrayaux
bio_visualization:
- rasmol
# - bio-linux-clcsequenceviewer # Awaiting fix
bio_proteomics:
all:
# Required for protk
- libxml2-dev
- libreadline-dev
- libxslt-dev
# Required for protvis
- python-virtualenv
- python-setuptools
- libpng12-dev
- python-dev
- libexpat1-dev
- libboost-dev
# Needed for TPP
- xsltproc
- libxml-sax-expat-perl
- libgd2-xpm-dev
- libbz2-dev
- gnuplot
# Needed for percolator
- libxerces-c3.1
- libxerces-c-dev
- xsdcxx
- libboost-dev
- libboost-filesystem-dev
- libboost-system-dev
- libsqlite3-0
- libboost-serialization-dev
- zlib1g-dev
- libboost-dev
# needed for 32bit execs distributed with searchgui.
# - ia32-libs ## Doesn't play well with dependencies of gnuplot, TODO: Find more specific lib.
# needed for building OpenMS
- libtool
- qt4-dev-tools
- libqtwebkit-dev
- libqtwebkit4
# Needed for psm-eval
- libyaml-dev
# Needed for RVM
- libbison-dev
- ncurses-dev
- automake
- libtool
- bison
- subversion
- libgdbm-dev
- libffi-dev
- libsqlite3-dev
- sqlite3
bio_proteomics_wine:
- wine
bio_utils:
- bio-linux-genquery
- bio-linux-keyring
- bio-linux-bldp-files
- bio-linux-sampledata
- bio-linux-taxinspector
# - bio-linux-xcut # hash mismatch
phylogeny_testing:
# new packages in testing (Debian 'wheezy')
all:
- debian-archive-keyring
- raxml
# - mrbayes-mpi broken, should eventually replace biolinux-mrbayes-multi
phylogeny_experimental:
# new packages in experimental
all:
- paml # should replace biolinux-paml
phylogeny:
all:
- phyml
- mrbayes
- njplot
- tree-puzzle
#- bio-linux-arb # problematic install questions
- bio-linux-archaeopteryx
- bio-linux-cytoscape
- bio-linux-dendroscope
- bio-linux-fastdnaml
#- bio-linux-happy # broken Depends: ia32-libs
- bio-linux-mesquite
- bio-linux-mrbayes
#- bio-linux-paml # Broken on 14.04
- bio-linux-omegamap
- bio-linux-qtlcart
#- bio-linux-splitstree # Broken on 14.04
- bio-linux-treeview
needs_64bit:
- bio-linux-fasttree
## Package lists imported from mi-deployment.
cloudman:
all:
# Required to install CloudMan-required Python libraries
- python-pip
# Required for communication between instances
- rabbitmq-server
# Required to handle data volumes (including LVM support)
- lvm2
- dmsetup
# - mdadm
- reiserfsprogs
- xfsprogs
# Required to compile nginx
- build-essential
#- gcc ## included in minimal
- libpcre3-dev
- libssl-dev
- stow
# Required for cluster-wide NFS file system
- nfs-kernel-server
- nfs-common
# Enable OpenMPI
- libopenmpi-dev
- libopenmpi1.3
- openmpi-bin
- openmpi-common
# Needed to enable updates for Galaxy
# - mercurial ## Included in minimal
# Required for compiling ProFTPd (must match installed PostgreSQL version!)
- postgresql-server-dev-9.3
# Actually not sure what of the following is really needed
- libboost-all-dev
- libreadline6-dev
# Required for s3fs
- libfuse-dev
- libfuse2
- pkg-config
- libcurl4-openssl-dev
- libxml2-dev
- mime-support
# Required for novnc
- vnc4server
- glusterfs-client
ubuntu_quantal:
# Required to get HTCondor, not available on 12.04 (latest LTS release).
- condor
galaxy:
all:
- postgresql
- gfortran
- default-jdk
- python-rpy
- xvfb
# Required by Freebayes
- cmake
# Required by BWA
- zlib1g-dev
# Required by Samtools
- libncurses5-dev
# Required by Compute q-values
- liblzma-dev
# Parallel file download (used by the Galaxy ObjectStore)
- axel
# Required by various R modules
- tcl-dev
# Required by various R modules
- tk-dev
# Required by RGalaxy
- imagemagick
- pdfjam
- python-scipy
- libsparsehash-dev
# Latest python-rpy not currently compatible with R 3.0.1 at least on precise (presumably
# quantal as well), hack below is to specify an older version of R compabile with python-rpy.
#- r-base
#- r-base-core
#- r-base-dev
- r-cran-lattice
- r-cran-qvalue
# Required by HVIS
- r-bioc-hilbertvis
ubuntu_quantal:
- "r-base-core=3.0.0-2quantal"
- "r-base-dev=3.0.0-2quantal"
ubuntu_precise:
- "r-base-core=3.0.0-2precise"
- "r-base-dev=3.0.0-2precise"
galaxyp:
all:
# Required for protk
- libxml2-dev
- libreadline-dev
- libxslt-dev
# Required for protvis
- python-virtualenv
- python-setuptools
- libpng12-dev
- python-dev
- libexpat1-dev
- libboost-dev
# Needed for TPP
- xsltproc
- libxml-sax-expat-perl
- libgd2-xpm-dev
- libbz2-dev
- gnuplot
# Needed for percolator
- libxerces-c3.1
- libxerces-c-dev
- xsdcxx
- libboost-dev
- libboost-filesystem-dev
- libboost-system-dev
- libsqlite3-0
- libboost-serialization-dev
- zlib1g-dev
- libboost-dev
# needed for 32bit execs distributed with searchgui.
# - ia32-libs ## Doesn't play well with dependencies of gnuplot, TODO: Find more specific lib.
# needed for building OpenMS
- libtool
- qt4-dev-tools
- libqtwebkit-dev
- libqtwebkit4
# Needed for nbic galaxy database utilities
- liblog-log4perl-perl
- libswiss-perl
# Needed for psm-eval
- libyaml-dev
# Needed for RVM
- libbison-dev
- ncurses-dev
- automake
- libtool
- bison
- subversion
- libgdbm-dev
- libffi-dev
- libsqlite3-dev
- sqlite3
# To do -- in Deb Med but not propogated
# squizz
# biomaj
#
# To Add -- need packages
# from bioperl-max:
# hyphy
# bioperl-db
# more perl modules
# from bio-linux:
# Celera Assembler
# lamarc - not available just now (22/6/10)
# peptidemapper
# pftools
# transterm
# Others:
# mdust
# IGV
# trimpoly
# blast2go
# sputnik: microsattelites
# GenomeView
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