packages.yaml

---
# 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
    - sysstat
    - iotop
    - iftop
    - nmon
  editors:
    - vim
    # don't put in emacs, as it pulls in X
  version_control:
    - git-core
    - cvs
    - subversion
    - mercurial
    - bzr
    - darcs
  build:
    - make
    - gcc
    - g++
    - gfortran
    - patch
    - cmake
    - swig
    - ant
    # Required by cloud-init on Ubuntu 12.04
    - software-properties-common
    - python-prettytable
    - libpam0g-dev
  util:
    - axel
    - rsync
    - openssh-server
    - screen
    - unzip
    - less
    - ipython
    - atop
  network:
    - curl
    - wget
desktop:
  #Packages to support a remote desktop
  all:
    - gnome-panel
    - gnome-system-tools
    - synaptic
    - software-center
    - freenx-server
    - 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:
  - xfce4
  - vnc4server
  - firefox
programming:
  editors:
    - emacs
    - emacs-goodies-el
    - emacsen-common
    - exuberant-ctags
    - gedit
  documentation:
    - texlive-latex-base
    - texlive-latex-recommended
    - texlive-latex-extra
  build:
    - swig
    - cmake
    - libcurl4-openssl-dev
    - libxml2
    - libxml2-dev
    - libxslt1-dev
    - libxslt1.1
    - libgsl0-dev
    - libgsl0ldbl
    - gsl-bin
    - xfsprogs
    - libc6-dev
    - libzip-dev
    - libbz2-dev
    - zlib1g-dev
    - xz-utils
    - liblzma-dev
    - libgtk2.0-dev
    - libncurses5-dev
    - zlib1g-dev
    - libssl-dev
    - libpcre3-dev
    - libreadline-dev
    - mime-support
    - uuid
    - uuid-dev
    - gcc
    - g++
    - gfortran
    - stow
    - rsync
    - python-software-properties
    - protobuf-compiler
  filesystem:
    - libfuse-dev
    - fuse-utils
  libraries:
    - libatlas-base-dev
    #- libatlas-dev
    - libblas-dev
    - liblapack-dev
    - libeigen3-dev
    - tcl-dev
    - tk-dev
    - imagemagick
    - pdfjam
    - libsparsehash-dev
    - xvfb
    - libboost-dev
    - libboost-python-dev
    - libboost-thread-dev
    - libgd2-xpm
    - libgd2-xpm-dev
    - libgnomecanvas2-0
    - libgnomecanvas2-dev
    - libgnomevfs2-0
    - libgnomevfs2-dev
    - libgnomeui-0
    - libgnomeui-dev
    - libpango1.0-0
    - libpango1.0-dev
    - libx11-dev
    - libfreetype6-dev
    - libcgi-session-perl
    - libclass-base-perl
  packaging:
    - build-essential
    - devscripts
    - debhelper
    - dh-make
    - pbuilder
    - unzip
  virtual:
    # - virtualbox-4.1
    - dkms
  util:
    - mc
    - tree
    - screen
    - time
    - fdupes
  network:
    - lynx
    - traceroute
  lang:
    - aspell
    - dictionaries-common
    - libaspell-dev
# Note that the following Cloudera hadoop installation is for test
# purposes "inside the instance" only, Amazon already provides a
# production-ready Elastic MapReduce platform:
# http://aws.amazon.com/elasticmapreduce/
distributed:
  all:
    - rabbitmq-server
    - nfs-kernel-server
    - nfs-common
    # - hadoop-0.20
    # - hadoop-pig
    # - hadoop-hive
    # - libhdfs0-dev
    # - hadoop-0.20-pipes
    # - hadoop-0.20-source
    - libopenmpi-dev
    - openmpi-bin
    - libzmq-dev
    - libfuse-dev
  # only for oneiric 11.10
  ubuntu_oneiric:
    - libmpich2-3
    - libmpich2-dev
    - mpich2
amazon:
  - s3cmd
  - euca2ools
  - ec2-ami-tools
  - ec2-api-tools
  # - python-vm-builder-ec2
python:
  meta:
    - python
    - python-dev
    - python-setuptools
    - python-distutils-extra
    # - python3
    # - python3-dev
    - python-pip
  wrappers:
    - python-rpy
ruby:
  - ruby1.9.1 # default Ruby install
  - ruby1.9.1-dev
  # - ruby1.8
  # - ruby1.8-dev
r:
  - r-base
  - r-base-core
  - r-base-dev
  # - r-base-html
perl:
  - perl
  - bioperl
  - libperl-dev
  - perl-modules
  - perl-tk
  - parrot
  - parrot-devel
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-6-jdk
  # - openjdk-6-jre
  - openjdk-7-jdk
  - openjdk-7-jre
  - ant
  - libbiojava-java
  - libbiojava-java-demos
  # - eclipse
  - maven2
  - libjline-java
  - libjhdf5-java
  - clojure
  - jruby
  - jython
  - scala
  - scala-library
erlang:
  - erlang
  - erlang-base
  - erlang-dev
  - erlang-examples
  - erlang-manpages
  - erlang-mode
haskell:
  - ghc6
  - cabal-install
  - c2hs
databases:
  mysql:
    - mysql-client
    - mysql-common
    - mysql-server
    - libmysqlclient15-dev
  postgres:
    - postgresql
    - postgresql-client
    - postgresql-plpython-9.1
    # - postgresql-plperl-9.1
    - libpq-dev
  sqlite:
    - libsqlite0
    - libsqlite0-dev
    - libsqlite3-0
    - libsqlite3-dev
    - sqlite3
  document:
    # - libdb-dev
    # - mongodb-10gen
    # - couchdb
    # - tokyocabinet-bin
    # - libtokyocabinet9
    # - libtokyocabinet-dev
  hdf:
    # - libhdf5-7
    # - libhdf5-dev
php:
  - php5-fpm
  - php5-gd
  - php5-odbc
  - php5-pgsql
ftp:
  - vsftpd
drupal:
  - drush
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
  - emboss-data
  - emboss-lib
  - jemboss
  - 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
  - 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
  - bio-linux-prank
  - probcons
  - wise
bio_nextgen:
  - bio-linux-fastqc
  - fastx-toolkit
  - maq
  - plink
  - last-align
  - tabix
  - samtools # now up-to-date again
bio_sequencing:
  #- bio-linux-assembly-conversion-tools # broken Depends: bio-linux-staden
  - bio-linux-cap3
  - bio-linux-dust
  - bio-linux-lucy
  - bio-linux-mira
  - bio-linux-mira-3rd-party
  # - bio-linux-staden # broken Depends: ia32-libs
  # - bio-linux-stars # broken Depends: bio-linux-staden
  - 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-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 # 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_utils:
  - bio-linux-genquery
  - bio-linux-keyring
  - bio-linux-bldp-files
  - bio-linux-sampledata
  - bio-linux-taxinspector
  - bio-linux-xcut
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:
    - phylip
    - phyml
    - mrbayes
    - njplot
    - tree-puzzle
    - bio-linux-arb
    - 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
    - bio-linux-omegamap
    - bio-linux-qtlcart
    - bio-linux-splitstree
    - bio-linux-treeview
  needs_64bit:
    - bio-linux-fasttree
modules:  # currently installing environment modules from source; these are dependencies
  - tcl
  - tcl-dev
## 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-9.1
    # Actually not sure what of the following is really needed
    - libboost-all-dev
    - libreadline6-dev
    # Required for s3fs
    - libfuse-dev
    - libfuse2
    - fuse-utils
    - pkg-config
    - libcurl4-openssl-dev
    - libxml2-dev
    - mime-support
    # Required to get HTCondor
    - condor
    - glusterfs-client
    # Add some security against brute force ssh attacks
    - fail2ban
galaxy:
  all:
    - postgresql
    - gfortran
    - default-jdk
    - python-rpy
    - xvfb
    # Parallel file download (used by the Galaxy ObjectStore)
    - axel
    # Required by Freebayes
    - cmake
    # Required by BWA
    - zlib1g-dev
    # Required by Samtools
    - libncurses5-dev
    # Required by Compute q-values
    - liblzma-dev
    - r-base
    - r-base-core
    - r-base-dev
    - r-cran-lattice
    - r-cran-qvalue
    # Required by HVIS
    - r-bioc-hilbertvis
    # Required by various R modules
    - tcl-dev
    # Required by various R modules
    - tk-dev
    # Required by RGalaxy
    - imagemagick
    - pdfjam
    - python-scipy
    - libsparsehash-dev

# 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