version uengs2024

Dockerfile

@@ -25,7 +25,7 @@ RUN if [ -f "install.R" ]; then \
 WORKDIR /opt
 
 ##UCSC tools
-RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/*[wW]ig* /usr/local/bin/
+#RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/*[wW]ig* /usr/local/bin/
 
 # Trinity:
 #https://github.com/trinityrnaseq/trinityrnaseq
@@ -53,8 +53,8 @@ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/*[wW
 
 #install space ranger
 #WORKDIR /opt
-#RUN wget -O spaceranger-2.1.0.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.gz?Expires=1693974326&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=BEWx4GOU0Rbc~3N2-m5qvUbVUxT2i8q4PRco1rqrHh-C3U2KIHwJ9oQX5SxmYApDM-~ENtciSD80BPkJRDzY95sg8SZVzbpjDB9b-q1TrXvfZuKb8LT-7rryktZr1brEFacCxgFxKDotbEDsYJwVfqP0WOS~rWYfAPBM6Wkq-iZe1A0a8OtOC5VCI5vE1CRqNZOwRaDb9p06E-R7TLgcB9VFthdKIDd1jn2rTBj6ZocXJNJo9diQEDoZQ9P1ysU6c3drdQYC5Z1rpXvVUBiEa8dQUqF8JfN16z7DdyUwzoH~i0exNJtY2gJ44EmVNz6zw8keyOIpuPWfTV-1-MR0xg__" && \
-#  tar -xzvf spaceranger-2.1.0.tar.gz
+#RUN wget -O spaceranger-3.1.0.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.0.tar.gz?Expires=1725492623&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=Ur3tKIQ6v3wWbt287~eVW2CaKHgCasRKB7FIuq1lPrk9eVA7icpNdbVyR~LuWEml9UdNdwlg78rmRhH6k5EaMfcuTvN0-GHvgARdW2ZWvlu2jkV2LufN8sr9EmqAESHUABg253J1~9jpr8BJQgf92rEfNXu1b~mZM~zAMB19UkT44bNgxyX5M~99uhAnCVEfZoFv-Y-lQMB7bf2RAiLVfOu51BuT1jmdhmcK9by3tRRrCM1NtQOHU4xJWrblQQCHwPJ4TZXUhcmIxzAhIx1sV~UVST~OPgMLYDmBvu7Sjl6RqEXk~ZAfcKPKiZFfUhfORv0IiE0FFM1WsrhTF21T6g__" && \
+#  tar -xzvf spaceranger-3.1.0.tar.gz
 
 #ENV PATH=/opt/spaceranger-2.1.0/:"$PATH"
 
@@ -70,31 +70,37 @@ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/*[wW
 ENV PATH=/usr/games/:/home/rstudio/bin/:"$PATH"
 
 ## Install tools via conda
+USER rstudio
+WORKDIR /home/rstudio
+
+SHELL ["/bin/bash", "-c"]
 
-# install miniforge
-COPY install_miniforge.sh conda_clean_base.sh /opt/docker/bin/
-RUN bash /opt/docker/bin/install_miniforge.sh && \
-    bash /opt/docker/bin/conda_clean_base.sh
+RUN wget -O /tmp/Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" 
+RUN bash /tmp/Miniforge3.sh -b -p /home/rstudio/conda && \
+    rm /tmp/Miniforge3.sh && \
+    source /home/rstudio/conda/etc/profile.d/conda.sh && \
+    conda update -n base -c conda-forge conda && \
+    conda clean -a -y
 
 ### Install conda env for user 'rstudio'
-USER rstudio
-WORKDIR /home/rstudio
 
-##COPY --chown=rstudio environment_ngs.yml /opt/environment_ngs.yml 
-COPY --chown=rstudio environment_rnaseq.yml /opt/environment_rnaseq.yml
-##
+COPY environment_uengs.yml /opt/environment_uengs.yml
 ##
-RUN /opt/conda/bin/conda env create -f /opt/environment_rnaseq.yml && \
-    /opt/conda/bin/conda clean -a -y
-###RUN conda env create -f /opt/environment_ngs.yml && \
-###    conda clean -a -y
-##
-RUN echo "conda activate rnaseq" >> /home/rstudio/.bashrc
-###RUN echo "conda activate ngs" >> /home/rstudio/.bashrc
+RUN source /home/rstudio/conda/etc/profile.d/conda.sh &&\
+    conda env create -f /opt/environment_uengs.yml && \
+    conda clean -a -y
+
+
+COPY bashrc_ext.txt /tmp/bashrc_ext.txt
+RUN cat  /tmp/bashrc_ext.txt >> /home/rstudio/.bashrc
+
 ##
 ##
 ## Required for s6-supervise exec at container runtime init
 USER root
+
+RUN ln -s  /home/rstudio/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh 
+
 ##
 ### Optional
 WORKDIR /root/app-recipe
\ No newline at end of file

bashrc_ext.txt

+
+#clone conda envs
+conda activate base
+
+
+if [ ! -f /home/rstudio/.conda/clone_ok ]; then
+  
+  (conda create -p /home/rstudio/conda/envs/spatial --clone /home/rstudio/ifbdata/ueens_lyon_ngs24/.conda/envs/spatial_init > /home/rstudio/.conda/clone_spatial.log && \
+  conda create -p /home/rstudio/conda/envs/meso --clone /home/rstudio/ifbdata/ueens_lyon_ngs24/.conda/envs/meso_init > /home/rstudio/.conda/clone_meso.log && \
+  conda create -p /home/rstudio/conda/envs/chipseq --clone /home/rstudio/ifbdata/ueens_lyon_ngs24/.conda/envs/chipseq_init > /home/rstudio/.conda/clone_chipseq.log && \
+  conda create -p /home/rstudio/conda/envs/scrnaseq --clone /home/rstudio/ifbdata/ueens_lyon_ngs24/.conda/envs/scrnaseq_init > /home/rstudio/.conda/clone_scrnaseq.log &)
+  
+  touch /home/rstudio/.conda/clone_ok
+fi

conda_clean_base.sh

 #!/usr/bin/bash -eu
 
 # clean default conda environment (only keep the bare minimum)
-find /opt/conda/ -name '*.a' -delete && \
-find /opt/conda/ -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
-find /opt/conda/ -mindepth 1 -maxdepth 1 -type d \( -name "bin" -o -name "lib" -o -name "etc" \) -prune -o -exec rm -rf '{}' '+' && \
-find /opt/conda/bin -type f -size +100k ! -name "python3.10" -delete && \
-find /opt/conda/lib/ -mindepth 1 -maxdepth 1 -type d ! -name "python3.10" -exec rm -rf '{}' '+' && \
-rm -rf /opt/conda/lib/python3.10/site-packages/pip /opt/conda/lib/python3.10/idlelib /opt/conda/lib/python3.10/ensurepip && \
-find /opt/conda/lib/python3.10/site-packages -name '*.pyx' -delete && \
-rm -rf /opt/conda/lib/python3.10/site-packages/uvloop/loop.c
+find /home/rstudio/.conda/ -name '*.a' -delete && \
+find /home/rstudio/.conda/ -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
+find /home/rstudio/.conda/ -mindepth 1 -maxdepth 1 -type d \( -name "bin" -o -name "lib" -o -name "etc" \) -prune -o -exec rm -rf '{}' '+' && \
+find /home/rstudio/.conda/bin -type f -size +100k ! -name "python3.10" -delete && \
+find /home/rstudio/.conda/lib/ -mindepth 1 -maxdepth 1 -type d ! -name "python3.10" -exec rm -rf '{}' '+' && \
+rm -rf /home/rstudio/.conda/lib/python3.10/site-packages/pip /home/rstudio/.conda/lib/python3.10/idlelib /home/rstudio/.conda/lib/python3.10/ensurepip && \
+find /home/rstudio/.conda/lib/python3.10/site-packages -name '*.pyx' -delete && \
+rm -rf /home/rstudio/.conda/lib/python3.10/site-packages/uvloop/loop.c

environment_rnaseq.yml

@@ -4,14 +4,10 @@ channels:
   - bioconda
 dependencies:
   - seqtk
-  - bioawk
-  - sra-tools
-  - parallel-fastq-dump=0.6.7
   - fastp=0.23.4
   - salmon=1.10.3
   - star=2.7.11b
   - htseq=2.0.5
-  - subread=2.0.6
   - blast=2.16.0
   - fastqc=0.12.1
   - multiqc=1.24

environment_uengs.yml

+name: uengs
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - fastqc=0.12.1
+  - multiqc=1.24
+  - fastp
+  - cutadapt
+  - datamash
+  - seqtk

install.R

 options(Ncpus = parallel::detectCores())
+options(repos = c(CRAN = "https://cran.rstudio.com"))
 
 # Installation of standard R packages
-install.packages(c('remotes',
-                   'Seurat',
-                   'mvoutlier',
-                   'gprofiler2',
-                   'preseqR'))
+install.packages(c("remotes",
+                   "Seurat",
+                   "mvoutlier",
+                   "preseqR"))
 
 # Installation of packages with BiocManager
-install.packages('BiocManager')
+install.packages("BiocManager")
 BiocManager::install(
-    c('tximport',
-      'biomaRt',
-      'clusterProfiler',
-      'ComplexHeatmap',
-      'DESeq2',
-      'EnhancedVolcano',
-      'ggpubr',
-      'apeglm',
-      'scater',
-      'rhdf5',
-      'idr'
-      ), ask = FALSE)
+    c("biomaRt",
+      "clusterProfiler",
+      "apeglm",
+      "scater",
+      "rhdf5",
+      "idr"
+    ), ask = FALSE)
+
+
+BiocManager::install(c("eisaR",
+                       "BSgenome",
+                       "fishpond",
+                       "GenomicFeatures"))
+install.packages("devtools")
+
+devtools::install_github("COMBINE-lab/roe")
 
 # Install R package from GitHub
 #remotes::install_github("satijalab/seurat-data", "seurat5", quiet = TRUE)
 #remotes::install_github("satijalab/azimuth", "seurat5", quiet = TRUE)
 #remotes::install_github("satijalab/seurat-wrappers", "seurat5", quiet = TRUE)
+
+#Serat Wrapper
+install.packages(c("hwriter",
+                   "RcppParallel",
+                   "latticeExtra"))
+
+BiocManager::install("dada2")
\ No newline at end of file

install_miniforge.sh

@@ -13,14 +13,14 @@ export condapkg="https://github.com/conda-forge/miniforge/releases/download/${mi
 
 # Install the latest miniforge with Python3
 curl -s -L $condapkg > miniforge.sh
-bash miniforge.sh -b -p /opt/conda
+bash miniforge.sh -b -p /home/rstudio/conda/
 rm -f miniforge.sh
 
 # Work around TLS issues while updating conda's python and retrieving channel notices
 export CONDA_NUMBER_CHANNEL_NOTICES="0"
-touch /opt/conda/conda-meta/pinned
-ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh
-source /opt/conda/etc/profile.d/conda.sh
+touch /home/rstudio/.conda/conda-meta/pinned
+ln -s /home/rstudio/.conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh
+source /home/rstudio/.conda/etc/profile.d/conda.sh
 conda activate
 conda config --set show_channel_urls True
 conda config --set channel_priority strict
@@ -33,8 +33,3 @@ mamba update --yes --all
 # Clean to reduce image size
 conda clean -aftipy
 conda deactivate
-
-# custom user gets permission to write in the conda dir
-if id "rstudio" >/dev/null 2>&1; then
-    chown -R rstudio:rstudio /opt/conda
-fi