Setup (perl dependencies) and onbuild instructions for maker image
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The full context of this image can be found here.
Set up Docker image to include external software on-build - this assumes the files maker.tar.gz and repeatmaskerlibraries.tar.gz to be present in your working directory.
docker build -t chrishah/premaker-plus:18-onbuild --file Dockerfile_onbuild .
Include external software on-build -
docker build -t maker-full:v2.31.10 --file Dockerfile_maker_onbuild .
Save the container.
docker save maker-full:v2.31.10 | gzip > maker-full-v2.31.10.tar.gz
Build external software/databases outside the container:
#Build the container
docker build -t chrishah/premaker-plus:18 --file ./Dockerfile_noonbuild .
#Build Repeatmasker library
docker run --rm -v $(pwd):/in -w /in chrishah/premaker-plus:18 sh ./setup_Repeatmasker.sh src/ external/RepBaseRepeatMaskerEdition-20181026.tar.gz
#Build maker
docker run --rm -v $(pwd):/in -w /in chrishah/premaker-plus:18 sh ./setup_maker.sh src/ external/maker-2.31.10.tgz
After this you can run maker like so:
docker run --rm -v $(pwd):/in -w /in chrishah/premaker-plus:18 ./src/maker/bin/maker -v
If you want to include the newly built repeat libraries do this:
docker run --rm -v $(pwd)/src/RepeatMasker:/usr/local/RepeatMasker -v $(pwd):/in -w /in chrishah/premaker-plus:18 ./src/maker/bin/maker -v
If you want to include genemark as well, you can call the container like that (assumes you have a directory gm_et_linux_64 with all Genemark executables in the external directory):
docker run --rm -v $(pwd)/src/RepeatMasker:/usr/local/RepeatMasker -v $(pwd)/external/gm_et_linux_64/:/usr/local/Genemark -v $(pwd):/in -w /in chrishah/premaker-plus:18 ./src/maker/bin/maker -v
Content type
Image
Digest
Size
718.8 MB
Last updated
over 4 years ago
docker pull chrishah/premaker-plus:18-0d9787e