diff --git a/Dockerfile b/Dockerfile index ffef33215219ba08994b9ce185f1c47329cb2f81..2801363a58d02fc39b43ef56b902f5321be4d9b9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/tidyverse:4.4.1 +FROM rocker/tidyverse:4.4.3 USER root WORKDIR /root/app-recipe @@ -16,9 +16,9 @@ RUN if [ -f "apt.txt" ]; then \ # Install R packages USER root -COPY install.R . -RUN if [ -f "install.R" ]; then \ - Rscript install.R; \ +COPY install_rnaseq.R . +RUN if [ -f "install_rnaseq.R" ]; then \ + Rscript install_rnaseq.R; \ fi # Install tools from source @@ -84,15 +84,15 @@ RUN bash /tmp/Miniforge3.sh -b -p /home/rstudio/conda && \ ### Install conda env for user 'rstudio' -COPY environment_uengs.yml /opt/environment_uengs.yml +COPY environment_rnaseq.yml /opt/environment_rnaseq.yml ## RUN source /home/rstudio/conda/etc/profile.d/conda.sh &&\ - conda env create -f /opt/environment_uengs.yml && \ + conda env create -f /opt/environment_rnaseq.yml && \ conda clean -a -y -COPY bashrc_ext.txt /tmp/bashrc_ext.txt -RUN cat /tmp/bashrc_ext.txt >> /home/rstudio/.bashrc +COPY bashrc_ext_rnaseq.txt /tmp/bashrc_ext_rnaseq.txt +RUN cat /tmp/bashrc_ext_rnaseq.txt >> /home/rstudio/.bashrc ## ## diff --git a/bashrc_ext_rnaseq.txt b/bashrc_ext_rnaseq.txt new file mode 100644 index 0000000000000000000000000000000000000000..9256da4f5bb8c8c1514c573ab8fdefbfb43c54cd --- /dev/null +++ b/bashrc_ext_rnaseq.txt @@ -0,0 +1,3 @@ + +#activate conda env +conda activate rnaseq \ No newline at end of file diff --git a/bashrc_ext.txt b/bashrc_ext_uengs.txt similarity index 100% rename from bashrc_ext.txt rename to bashrc_ext_uengs.txt diff --git a/build_docker.sh b/build_docker.sh index 9b7f85930bd0b3ec730a4ebc2655f3f7ca8fd682..8305faa566b883fde993c977d943f24341f5e196 100644 --- a/build_docker.sh +++ b/build_docker.sh @@ -2,7 +2,7 @@ set -euo pipefail +o nounset IMAGE_NAME="tp_ngs" -TAG="v2024.2" +TAG="v2025.1" REPO=carinerey/$IMAGE_NAME:$TAG DOCKERFILE_DIR="." diff --git a/environment_rnaseq.yml b/environment_rnaseq.yml index b2932f135de6c2d90caed15e2c274408704b425e..6d049c0487a6abe02cc99d1dd97f682fcecff778 100644 --- a/environment_rnaseq.yml +++ b/environment_rnaseq.yml @@ -4,13 +4,13 @@ channels: - bioconda dependencies: - seqtk - - fastp=0.23.4 + - fastp=0.24.0 - salmon=1.10.3 - star=2.7.11b - htseq=2.0.5 - blast=2.16.0 - fastqc=0.12.1 - - multiqc=1.24 - - samtools=1.20 + - multiqc=1.27.1 + - samtools=1.21 - bamtools=2.5.2 - bedtools=2.31.1 diff --git a/install_rnaseq.R b/install_rnaseq.R new file mode 100644 index 0000000000000000000000000000000000000000..9c09ab7dabc92fff382586a15ad05808657fbf35 --- /dev/null +++ b/install_rnaseq.R @@ -0,0 +1,19 @@ +options(Ncpus = parallel::detectCores()) +options(repos = c(CRAN = "https://cran.rstudio.com")) + +# Installation of standard R packages +install.packages(c("remotes", "devtools")) + +# Installation of packages with BiocManager +install.packages("BiocManager") +BiocManager::install( + c("biomaRt", + "clusterProfiler", + "DESeq2", + "EnhancedVolcano", + "ggpubr", + "apeglm", + "scater", + "rhdf5", + "idr" + ), ask = FALSE) diff --git a/install.R b/install_uengs.R similarity index 100% rename from install.R rename to install_uengs.R