/premaker-plus-docker

Docker image as base for building full MAKER image

Primary LanguagePerl

premaker-plus-docker

Docker image as base for building full MAKER image, plus dependencies and third party software

In detail, the image is set up with:

  • Ubuntu 18.04
  • perl 5.26.1
  • Python 3.6.6
  • blast 2.6.0+
  • hmmer 3.1b2
  • Augustus 3.3
  • BUSCO 3.0.2
  • R 3.4.4
    • ggplot2 3.1.0
  • exonerate 2.4.0
  • SNAP (2017-05-17 - git commit: a89d68e8346337c155b99697389144dfb5470b0f)
  • RMBlastn 2.2.28
  • trf 407b
  • RepeatScout 1.0.5
  • RepeatMasker 4.0.7
  • RepeatModeler 1.0.10
  • perl dependencies for MAKER
    • DBI
    • DBD::SQLite
    • forks
    • forks::shared
    • File::Which
    • Perl::Unsafe::Signals
    • Bit::Vector
    • Inline::C
    • IO::All
    • IO::Prompt

The image can be pulled from Dockerhub (note the tag) via:

docker pull chrishah/premaker-plus-docker:v26112018

or built within the base directory of this repo, e.g. via:

docker build --network=host -t chrishah/premaker-plus-docker .

Build the fully functioning MAKER image

You'll need two more things in your working directory:

  • A copy of the latest Repbase-derived RepeatMasker libraries, renamed to repeatmaskerlibraries.tar.gz
    • this requires free (for academic purposes) registration
    • once registered, download the latest version, e.g. via:
wget --user your-user-name \
    --password your-password \
    -O repeatmaskerlibraries.tar.gz \
    https://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20181026.tar.gz
  • a copy of the MAKER archive (renamed to maker.tar.gz)
    • this again requires free (for academic purposes) registration

Once you have all this you can create a Dockerfile,

echo -e "FROM chrishah/premaker-plus-docker:v26112018" > Dockerfile-maker-plus

and build the functioning MAKER image:

docker build --network=host -t your-maker-plus --file Dockerfile-maker-plus .

Or you can use the Dockerfile dockerfiles/Dockerfile-maker-plus-onbuild (which is exactly the above), to build the functioning MAKER image via:

docker build --network=host -t your-maker-plus --file dockerfiles/Dockerfile-maker-plus-onbuild .

The above was tested with with:

  • MAKER v2.31.10
  • MAKER v3.01.02-beta
  • Repbase Repeatmasker Edition 20181026