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