builds

ubuntu20.04/basic:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) -t ubuntu20.04/basic:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/basic --pull

ubuntu16.04/basic:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) -t ubuntu16.04/basic:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/basic/16.04 --pull

debian_bullseye-slim/basic_anaconda3:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) -t ubuntu20.04/basic_anaconda3:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/basic/basic_anaconda3 --pull

docker build --build-arg CACHEBUST=$(date +%s) -t basic_anaconda3/dms_tools2:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/dms_tools2

ubuntu20.04/pbmpi:latest

docker build -t ubuntu20.04/pbmpi:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi

ubuntu20.04/pbmpi_mapstats:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/pbmpi_mapstats:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi/mapstats

ubuntu20.04/pbmpi_mutselaacdeg:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/pbmpi_mutselaacdeg:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi/mutselaacdeg

ubuntu20.04/coevol:latest

docker build -t ubuntu20.04/coevol:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/coevol

ubuntu20.04/phylobayes:latest

docker build -t ubuntu20.04/phylobayes:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes

ubuntu20.04/phylobayes_mapstats:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/phylobayes_mapstats:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes/mapstats

ubuntu20.04/lfp:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/lfp:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/LikelihoodFreePhylogenetics

ubuntu20.04/codeml:latest

docker build -t ubuntu20.04/codeml:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/codeml

ubuntu20.04/bayescode_chronogram:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_chronogram:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode

ubuntu20.04/bayescode_mutselaa:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_mutselaa:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode/mutselaa

ubuntu20.04/bayescode_mutselaac:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_mutselaac:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode/mutselaac

ubuntu20.04/bayescode_mutselc:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_mutselc:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode/mutselc

from MACSE https://github.com/ranwez/MACSE_V2_PIPELINES ** new version available **

docker build -t ubuntu16.04/macse:latest https://github.com/ranwez/MACSE_V2_PIPELINES.git#master:/OMM_MACSE/V11_05b_FREEZED -f OMM_MACSE_V11.05_docker.def

ubuntu16.04/macse:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu16.04/macse:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/macse

from pasteur evolbioinfo https://github.com/evolbioinfo

evolbioinfo/iqtree:v2.2.0

docker pull evolbioinfo/iqtree:v2.2.0

ubuntu20.04/iqtree:latest

docker build -t ubuntu20.04/iqtree:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/iqtree

ubuntu20.04/fasttree:latest

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/fasttree:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/fasttree

staphb/treemmer:latest from https://hub.docker.com/r/staphb/treemmer

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/treemmer https://github.com/Simonll/docker.git#develop:/dockerfiles/treemmer/

ubuntu20.04/revbayes:latest

docker build -t ubuntu20.04/revbayes:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/revbayes

r-base4.1.0/revbayesplus:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) --build-arg CACHEBUST=$(date +%s) -t r-base4.1.0/revbayesplus:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/revbayes/r-base/ --pull

ubuntu20.04/ncbi-datasets:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/ncbi-datasets https://github.com/Simonll/docker.git#develop:/dockerfiles/ncbi-datasets/

run interactive docker session

docker run --rm -v  $PWD:/data -it ubuntu20.04/revbayes:latest

connect to container with docker

Dev Containers: Attach to running container

R CRAN

r-base4.1.0/abc:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) --build-arg CACHEBUST=$(date +%s) -t r-base3.6.3/abc:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/r-base-abc --pull

r-base/phytools:latest

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) --build-arg CACHEBUST=$(date +%s) -t r-base3.6.3/phytools:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/r-base-phytools --pull

buchfink/diamond https://github.com/bbuchfink/diamond/

conda update diamond

busco

docker pull ezlabgva/busco:v5.5.7_cv1

biocontainers/buscov5.5.0:latest

YOURGROUPNAME="XXX"
docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) --build-arg GROUP_NAME=$YOURGROUPNAME -t biocontainers/buscov5.5.0:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/busco/

rstudio:4.2.2

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/rstudio:4.2.2 https://github.com/Simonll/docker.git#develop:/dockerfiles/rstudio/4.2.2 --pull

serving rstudio using portfowarding

ssh -L 8787:localhost:8787 user@server

override entrypoint with --entrypoint /bin/bash

docker run --rm -v  $PWD:/data -it  --entrypoint /bin/bash r-base3.6.3/phytools:latest

pandoc

• https://hub.docker.com/r/pandoc/minimal

for pruning docker cache

if something like this happens "E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2.9_amd64.deb 404 Not Found [IP: XXX.XXX.XXX.XXX 80]" you need to re-build the image from scratch

docker system prune -a