<commit_before>---
# 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
  build:
    - make
    - gcc
    - g++
    - gfortran
    - patch
    - cmake
    - swig
  util:
    - axel
    - gawk
    - rsync
    - openssh-server
    - 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
    - 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:
    - xfsprogs
    - stow
    - rsync
    - python-software-properties
    - protobuf-compiler
    - libgtk2.0-dev
    - stow
    - rsync
    - python-software-properties
    - protobuf-compiler
  filesystem:
    - libfuse-dev
    - fuse-utils
  libraries:
    - 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
  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
    - libopenmpi-dev
    - openmpi-bin
    - libzmq-dev
    - libfuse-dev
  # only for oneiric 11.10
  ubuntu_oneiric:
    - libmpich2-3
    - libmpich2-dev
    - mpich2
hadoop:
  - hadoop-0.20
  - hadoop-pig
  - hadoop-hive
  - libhdfs0-dev
  - hadoop-0.20-pipes
  - hadoop-0.20-source
amazon:
  - s3cmd
  - euca2ools
  - ec2-ami-tools
  - ec2-api-tools
  - python-vm-builder-ec2
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
  - ruby1.8
  - ruby1.8-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
  - libextutils-cbuilder-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-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
    - libtokyocabinet-dev
  hdf:
    - libhdf5-7
    - libhdf5-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
  - 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:<commit_msg>Remove perl cbuilder swapped into perl-modules and use debian mira packages. Fixes #78. Fixes #79.<commit_after>---
# 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
  build:
    - make
    - gcc
    - g++
    - gfortran
    - patch
    - cmake
    - swig
  util:
    - axel
    - gawk
    - rsync
    - openssh-server
    - 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
    - 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:
    - xfsprogs
    - stow
    - rsync
    - python-software-properties
    - protobuf-compiler
    - libgtk2.0-dev
    - stow
    - rsync
    - python-software-properties
    - protobuf-compiler
  filesystem:
    - libfuse-dev
    - fuse-utils
  libraries:
    - 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
  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
    - libopenmpi-dev
    - openmpi-bin
    - libzmq-dev
    - libfuse-dev
  # only for oneiric 11.10
  ubuntu_oneiric:
    - libmpich2-3
    - libmpich2-dev
    - mpich2
hadoop:
  - hadoop-0.20
  - hadoop-pig
  - hadoop-hive
  - libhdfs0-dev
  - hadoop-0.20-pipes
  - hadoop-0.20-source
amazon:
  - s3cmd
  - euca2ools
  - ec2-ami-tools
  - ec2-api-tools
  - python-vm-builder-ec2
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
  - ruby1.8
  - ruby1.8-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-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
    - libtokyocabinet-dev
  hdf:
    - libhdf5-7
    - libhdf5-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
  - 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-staden # broken Depends: ia32-libs
  # - bio-linux-stars # broken Depends: bio-linux-staden
  - bio-linux-tablet
  - mira-assembler
bio_annotation:
{'fraction_non_alphanumeric': 0.10704284514141697, 'fraction_numerical': 0.01813217586110333, 'mean_word_length': 1.964923204649232, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1959862', 'n_tokens_mistral': 5982, 'n_tokens_neox': 5718, 'n_words': 1075}