From 5b82872a2dc62d613001bdcef301503411e345c1 Mon Sep 17 00:00:00 2001 From: David Spencer <4720638+dhspence@users.noreply.github.com> Date: Wed, 7 Aug 2024 16:28:52 +0000 Subject: [PATCH] fixed rbio --- docker-bsseq/Dockerfile | 2 +- docker-rbioconductor/Dockerfile | 19 ++++- docker-rpy/Dockerfile | 15 ---- docker-rpy/env/basic-tools.yml | 25 ------ docker-rpy/scripts/conda_soft_links.sh | 10 --- docker-rstudio-python/.dir_bash_history | 12 --- docker-rstudio/.dir_bash_history | 104 ------------------------ 7 files changed, 16 insertions(+), 171 deletions(-) delete mode 100644 docker-rpy/Dockerfile delete mode 100644 docker-rpy/env/basic-tools.yml delete mode 100644 docker-rpy/scripts/conda_soft_links.sh delete mode 100755 docker-rstudio-python/.dir_bash_history delete mode 100755 docker-rstudio/.dir_bash_history diff --git a/docker-bsseq/Dockerfile b/docker-bsseq/Dockerfile index c6610e3..536d172 100644 --- a/docker-bsseq/Dockerfile +++ b/docker-bsseq/Dockerfile @@ -30,7 +30,7 @@ RUN apt-get update && apt-get -y install \ RUN R -e "install.packages('BiocManager'); BiocManager::install(version = '3.19')" # Install required R and Bioconductor packages -RUN R -e "install.packages(c('argparse', 'data.table', 'tidyverse', 'vcfR')); \ +RUN R -e "install.packages(c('argparse', 'data.table', 'dplyr' 'tidyverse', 'vcfR')); \ BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))" # Entry point for the container diff --git a/docker-rbioconductor/Dockerfile b/docker-rbioconductor/Dockerfile index c5b27e3..3bc92cd 100644 --- a/docker-rbioconductor/Dockerfile +++ b/docker-rbioconductor/Dockerfile @@ -8,6 +8,7 @@ RUN cp /usr/local/lib/R/site-library/littler/examples/installBioc.r /usr/local/b RUN apt-get update && apt-get -y install \ less \ curl \ + wget \ gzip \ lsof \ libz-dev \ @@ -17,10 +18,10 @@ RUN apt-get update && apt-get -y install \ libxml2-dev \ libxt6 \ libglpk-dev \ + libpcre2-dev \ + libdeflate-dev \ libmysqlclient21 \ - libcurl4-openssl-dev \ - python3 \ - python3-pip && \ + libcurl4-openssl-dev && \ apt-get clean # Install basic R packages @@ -28,7 +29,17 @@ RUN R -e "install.packages(c('argparse', 'data.table', 'dplyr', 'tidyverse', 'ti # Install Bioconductor and packages RUN R -e "install.packages('BiocManager'); BiocManager::install(version = '3.19')" -RUN R -e "BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))" +RUN R -e "BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit','rtracklayer'))" + +ENV CONDA_DIR /opt/conda +RUN cd /tmp && mkdir -p $CONDA_DIR && \ + wget "https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-24.3.0-0-Linux-x86_64.sh" && \ + bash Mambaforge-24.3.0-0-Linux-x86_64.sh -f -b -p $CONDA_DIR && \ + rm -f Mambaforge-24.3.0-0-Linux-x86_64.sh && \ + $CONDA_DIR/bin/mamba install -y --channel conda-forge --channel bioconda bcftools==1.20 htslib==1.20 samtools==1.20 bedtools=2.31 pandas==2.0.2 pybedtools==0.9.0 openpyxl==3.1.2 scipy==1.11.4 cython cyvcf2==0.30.28 pysam==0.22.1 statsmodels pyranges==0.0.129 pybigwig biotite && \ + $CONDA_DIR/bin/conda clean -y --all && \ + ln -s /opt/conda/bin/* /usr/local/bin/ + # Entry point for the container CMD ["bash"] \ No newline at end of file diff --git a/docker-rpy/Dockerfile b/docker-rpy/Dockerfile deleted file mode 100644 index 3fb4fbf..0000000 --- a/docker-rpy/Dockerfile +++ /dev/null @@ -1,15 +0,0 @@ -# Use the Rocker R image -FROM ghcr.io/dhslab/docker-rbioconductor:3.19 - -ARG MAMBA_VERSION="24.3.0-0" - -ENV CONDA_DIR /opt/conda -COPY env/*.yml /tmp/ -RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/download/${MAMBA_VERSION}/Miniforge3-$(uname)-$(uname -m).sh" && \ - bash Miniforge3-$(uname)-$(uname -m).sh -f -b -p /opt/conda && \ - rm -f Miniforge3-$(uname)-$(uname -m).sh && \ - $CONDA_DIR/bin/mamba env update -n base -f /tmp/basic-tools.yml && \ - $CONDA_DIR/bin/conda clean -y --all - -# Entry point for the container -CMD ["bash"] \ No newline at end of file diff --git a/docker-rpy/env/basic-tools.yml b/docker-rpy/env/basic-tools.yml deleted file mode 100644 index 50c3696..0000000 --- a/docker-rpy/env/basic-tools.yml +++ /dev/null @@ -1,25 +0,0 @@ -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - python - - pandas - - numpy - - pybedtools - - bedtools - - bcftools - - htslib - - samtools - - tabulate - - deeptools - - pip - - openpyxl - - scikit-misc - - scikit-learn - - zlib - - pip: - - polars - - pyranges - - gtfparse - - rpy2 diff --git a/docker-rpy/scripts/conda_soft_links.sh b/docker-rpy/scripts/conda_soft_links.sh deleted file mode 100644 index 148ea7a..0000000 --- a/docker-rpy/scripts/conda_soft_links.sh +++ /dev/null @@ -1,10 +0,0 @@ -# this loop to avoid overiding any existing soft-linked binary -link_path=$1 -for file in `ls $link_path` ; do - if [ -f /usr/local/bin/$file ] - then - : - else - ln -s ${link_path}/$file /usr/local/bin/$file - fi -done \ No newline at end of file diff --git a/docker-rstudio-python/.dir_bash_history b/docker-rstudio-python/.dir_bash_history deleted file mode 100755 index 020a392..0000000 --- a/docker-rstudio-python/.dir_bash_history +++ /dev/null @@ -1,12 +0,0 @@ -#1680744963 -cd docker-rstudio-python/ -#1680744985 -cp ../docker-hictools/Dockerfile . -#1680744987 -emacs Dockerfile -#1680745664 -exit -#1719843895 -cd ../docker-rstudio-python/ -#1719843900 -less Dockerfile diff --git a/docker-rstudio/.dir_bash_history b/docker-rstudio/.dir_bash_history deleted file mode 100755 index 822425b..0000000 --- a/docker-rstudio/.dir_bash_history +++ /dev/null @@ -1,104 +0,0 @@ -#1667439637 -cd docker-rstudio/ -#1667439640 -emacs Dockerfile -#1667443808 -exit -#1680047803 -cd docker-rstudio/ -#1680047807 -emacs Dockerfile -#1680048015 -cp /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680048018 -clar -#1680048026 -/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680048033 -cp /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile . -#1680048117 -less rstudio_4.2.2_mod.Dockerfile -#1680048171 -clear -#1680048179 -mv Dockerfile DockerfileOLD -#1680048190 -cp rstudio_4.2.2_mod.Dockerfile Dockerfile -#1680048194 -emacs Dockerfile -#1680048543 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio:latest)' -- --tag dhspence/docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680048626 -clear -#1680048627 -bjobs -#1680048629 -clear -#1680048667 -echo $USER -#1680048669 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio:latest)' -- --tag dhspence/docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680048857 -bjobs -#1680048859 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio:latest)' -- --tag dhspence/docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680049025 -bjobs -#1680049047 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(docker-rstudio:latest)' -- --tag docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680049163 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio:latest)' -- --tag dhspence/docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/ -#1680050152 -cp -r /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 . -#1680050159 -mv Dockerfile rocker-versioned2/ -#1680050189 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio:latest)' -- --tag dhspence/docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f $(readlink -f rocker-versioned2/Dockerfile) $(readlink -f rocker-versioned2/) -#1680050524 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio:latest)' -- --tag dhspence/docker-rstudio:latest --build-arg DEFAULT_USER=${USER} --no-cache -f /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680050620 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio)' -- --tag latest --build-arg DEFAULT_USER=${USER} --no-cache -f /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680050812 -bsub -G compute-dspencer -q general-interactive -Is -a 'docker_build(dhspence/docker-rstudio)' -f /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680050827 -bsub -G compute-dspencer -q general-interactive -Is -a "docker_build(dhspence/docker-rstudio)" -f /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680050856 -bsub -G compute-dspencer -q general-interactive -Is -a "docker_build(dhspence/docker-rstudio)" -- --tag latest --build-arg DEFAULT_USER=${USER} --no-cache -f /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2/dockerfiles/rstudio_4.2.2_mod.Dockerfile /storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/docker/rstudio/20220120/rocker-versioned2 -#1680053080 -cd docker-rstudio/ -#1680053083 -ls rocker-versioned2/ -#1680053097 -less rocker-versioned2/Dockerfile -#1680053111 -rm -f *~ -#1680053122 -mv rocker-versioned2/* . -#1680053800 -cd docker-rstudio/ -#1680053837 -cd .. -#1680216529 -cd docker-rstudio/ -#1680216536 -emacs Dockerfile -#1680721621 -cd dhslab-docker-images/docker-rstudio/ -#1680721629 -emacs Dockerfile -#1709752875 -cd git/dhslab-docker-images/docker-rstudio -#1709753221 -clear -#1719843481 -cd docker-rstudio -#1719843487 -ll -#1719843490 -abp Dockerfile -#1719843797 -abp rstudio_4.2.2_mod.Dockerfile -#1719843882 -clear -#1719843884 -ls ..