docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) -t ubuntu20.04/basic:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/basic --pull
docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) -t ubuntu16.04/basic:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/basic/16.04 --pull
docker build --build-arg USER_NAME=$(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
docker build -t ubuntu20.04/pbmpi:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/pbmpi_mapstats:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi/mapstats
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/pbmpi_mutselaacdeg:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi/mutselaacdeg
docker build -t ubuntu20.04/coevol:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/coevol
docker build -t ubuntu20.04/phylobayes:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/phylobayes_mapstats:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes/mapstats
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/lfp:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/LikelihoodFreePhylogenetics
docker build -t ubuntu20.04/codeml:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/codeml
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_chronogram:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_mutselaa:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode/mutselaa
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/bayescode_mutselaac:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/BayesCode/mutselaac
docker build --build-arg CACHEBUST=$(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
docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu16.04/macse:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/macse
from pasteur evolbioinfo https://github.com/evolbioinfo
docker pull evolbioinfo/iqtree:v2.2.0
docker build -t ubuntu20.04/iqtree:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/iqtree
docker build --build-arg CACHEBUST=$(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/
docker build -t ubuntu20.04/revbayes:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/revbayes
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
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/
docker run --rm -v $PWD:/data -it ubuntu20.04/revbayes:latest
Dev Containers: Attach to running container
docker build --build-arg USER_NAME=$(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
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
docker pull ezlabgva/busco:v5.5.7_cv1
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/
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
ssh -L 8787:localhost:8787 user@server
docker run --rm -v $PWD:/data -it --entrypoint /bin/bash r-base3.6.3/phytools:latest
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