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Commit f6133048 authored by Carine Rey's avatar Carine Rey
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update rnaseq2025

parent a2bc3056
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FROM rocker/tidyverse:4.4.1 FROM rocker/tidyverse:4.4.3
USER root USER root
WORKDIR /root/app-recipe WORKDIR /root/app-recipe
...@@ -16,9 +16,9 @@ RUN if [ -f "apt.txt" ]; then \ ...@@ -16,9 +16,9 @@ RUN if [ -f "apt.txt" ]; then \
# Install R packages # Install R packages
USER root USER root
COPY install.R . COPY install_rnaseq.R .
RUN if [ -f "install.R" ]; then \ RUN if [ -f "install_rnaseq.R" ]; then \
Rscript install.R; \ Rscript install_rnaseq.R; \
fi fi
# Install tools from source # Install tools from source
...@@ -84,15 +84,15 @@ RUN bash /tmp/Miniforge3.sh -b -p /home/rstudio/conda && \ ...@@ -84,15 +84,15 @@ RUN bash /tmp/Miniforge3.sh -b -p /home/rstudio/conda && \
### Install conda env for user 'rstudio' ### 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 &&\ 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 conda clean -a -y
COPY bashrc_ext.txt /tmp/bashrc_ext.txt COPY bashrc_ext_rnaseq.txt /tmp/bashrc_ext_rnaseq.txt
RUN cat /tmp/bashrc_ext.txt >> /home/rstudio/.bashrc RUN cat /tmp/bashrc_ext_rnaseq.txt >> /home/rstudio/.bashrc
## ##
## ##
......
#activate conda env
conda activate rnaseq
\ No newline at end of file
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...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
set -euo pipefail +o nounset set -euo pipefail +o nounset
IMAGE_NAME="tp_ngs" IMAGE_NAME="tp_ngs"
TAG="v2024.2" TAG="v2025.1"
REPO=carinerey/$IMAGE_NAME:$TAG REPO=carinerey/$IMAGE_NAME:$TAG
DOCKERFILE_DIR="." DOCKERFILE_DIR="."
......
...@@ -4,13 +4,13 @@ channels: ...@@ -4,13 +4,13 @@ channels:
- bioconda - bioconda
dependencies: dependencies:
- seqtk - seqtk
- fastp=0.23.4 - fastp=0.24.0
- salmon=1.10.3 - salmon=1.10.3
- star=2.7.11b - star=2.7.11b
- htseq=2.0.5 - htseq=2.0.5
- blast=2.16.0 - blast=2.16.0
- fastqc=0.12.1 - fastqc=0.12.1
- multiqc=1.24 - multiqc=1.27.1
- samtools=1.20 - samtools=1.21
- bamtools=2.5.2 - bamtools=2.5.2
- bedtools=2.31.1 - bedtools=2.31.1
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)
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