chore(version): Upgrade to 2.3.4

friendsofstrandseq · Jul 1, 2024 · 2c6daa4 · 2c6daa4
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diff --git a/github-actions-runner/Dockerfile-2.3.3.dockerfile b/github-actions-runner/Dockerfile-2.3.3.dockerfile
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+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="22effd6350726c78ed86abb188186be7228dec306b43048f6071c6359f7ee6b7"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.3/workflow/envs/ashleys_base.yaml
+#   prefix: /conda-envs/eba7cf011bffb12bcf25d066f6955913
+#   name: ashleys_base
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - samtools
+#     - tabix
+#     - bwa
+#     - sambamba
+#     - mosaicatcher
+#     # - alfred
+#     - ashleys-qc
+#     - pandas
+#     # PUBLISHDIR
+#     - rsync
+#     # MULTIQC
+#     - multiqc
+#     # Fix sklearn update
+#     - scikit-learn=1.2.2
+#     # Fix ashleys GH issue
+#     - python=3.10
+RUN mkdir -p /conda-envs/eba7cf011bffb12bcf25d066f6955913
+ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.3/workflow/envs/ashleys_base.yaml /conda-envs/eba7cf011bffb12bcf25d066f6955913/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.3/workflow/envs/ashleys_rtools.yaml
+#   prefix: /conda-envs/9b847fc31baae8e01dfb7ce438a56b71
+#   name: rtools
+#   channels:
+#     - conda-forge
+#     - bioconda
+#     - r
+#     - anaconda
+#   dependencies:
+#     # - bioconductor-biocparallel
+#     # - bioconductor-bsgenome
+#     # - bioconductor-bsgenome.hsapiens.ucsc.hg19
+#     # - bioconductor-bsgenome.hsapiens.ucsc.hg38
+#     # - bioconductor-fastseg
+#     # - bioconductor-genomicalignments
+#     - bioconductor-genomicranges
+#     # - bioconductor-rsamtools
+#     # - bioconductor-s4vectors
+#     - r-assertthat
+#     - r-base
+#     # - r-biocmanager
+#     - r-cowplot
+#     - r-data.table
+#     # - r-devtools
+#     # - r-doparallel
+#     # - r-foreach
+#     - r-ggplot2
+#     # - r-gtools
+#     - r-reshape2
+#     # - r-zoo
+#     # - r-dplyr
+#     # - r-mc2d
+#     # - r-pheatmap
+#     # - bioconductor-complexheatmap
+#     # - r-gplots
+#     - r-scales
+#     - r-rcolorbrewer
+#     # - r-stringr
+#     - r-cairo
+#     - fonts-anaconda
+#     # NEW
+#     - bioconductor-edger
+#     - r-r.utils
+#     # PLATE PLOT
+#     - r-dplyr
+#     - r-platetools
+#     - r-viridis
+#     # GC_correction
+#     - r-tidyr
+#     - r-ggpubr
+#     # SOLVE R lib issue
+#     - r-stringi=1.7.12
+RUN mkdir -p /conda-envs/9b847fc31baae8e01dfb7ce438a56b71
+ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.3/workflow/envs/ashleys_rtools.yaml /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml
+#   prefix: /conda-envs/5681728a49bd83ceed09ba194330c858
+#   channels:
+#     - bioconda
+#     - conda-forge
+#     - defaults
+#   dependencies:
+#     - bwa ==0.7.17
+RUN mkdir -p /conda-envs/5681728a49bd83ceed09ba194330c858
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml /conda-envs/5681728a49bd83ceed09ba194330c858/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml
+#   prefix: /conda-envs/08d4368302a4bdf7eda6b536495efe7d
+#   channels:
+#     - bioconda
+#     - conda-forge
+#     - defaults
+#   dependencies:
+#     - fastqc ==0.11.9
+RUN mkdir -p /conda-envs/08d4368302a4bdf7eda6b536495efe7d
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml /conda-envs/08d4368302a4bdf7eda6b536495efe7d/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/mc_base.yaml
+#   prefix: /conda-envs/13317d3185b8c4c0305fe98c6a708486
+#   name: mc-base
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - pandas
+#     - intervaltree
+#     - scipy
+#     - pysam
+#     - tqdm
+#     - perl
+#     - pypdf2
+#     - parmap
+#     # NEW
+#     - pyyaml
+#     - seaborn
+#     - matplotlib
+#     # SOLVE se-pe detection
+#     - samtools
+#     # ArbiGent Hufsah deps
+#     - pytables
+#     - xopen
+#     # Fix jbrowse tracks generation
+#     - pybigwig
+RUN mkdir -p /conda-envs/13317d3185b8c4c0305fe98c6a708486
+COPY workflow/envs/mc_base.yaml /conda-envs/13317d3185b8c4c0305fe98c6a708486/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/mc_bioinfo_tools.yaml
+#   prefix: /conda-envs/f251d84cdc9f25d0e14b48e780261d66
+#   name: mc-bioinfo-tools
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - bcftools
+#     - freebayes
+#     - mosaicatcher
+#     - samtools
+#     - tabix
+#     - whatshap
+RUN mkdir -p /conda-envs/f251d84cdc9f25d0e14b48e780261d66
+COPY workflow/envs/mc_bioinfo_tools.yaml /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/rtools.yaml
+#   prefix: /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33
+#   name: rtools
+#   channels:
+#     - bioconda
+#     - conda-forge
+#     - r
+#     - anaconda
+#   dependencies:
+#     # # NEW
+#     - strandphaser
+#     # ###############
+#     - bioconductor-biocparallel
+#     - bioconductor-bsgenome
+#     - bioconductor-bsgenome.hsapiens.ucsc.hg38
+#     - bioconductor-complexheatmap
+#     # - bioconductor-fastseg
+#     - bioconductor-genomicalignments
+#     - bioconductor-genomicranges
+#     - bioconductor-rsamtools
+#     # - bioconductor-s4vectors
+#     - fonts-anaconda
+#     - r-assertthat
+#     - r-base
+#     - r-biocmanager
+#     - r-cairo
+#     - r-cowplot
+#     - r-data.table
+#     - r-devtools
+#     - r-doparallel
+#     - r-dplyr
+#     - r-foreach
+#     - r-ggplot2
+#     - r-gplots
+#     - r-gtools
+#     - r-mc2d
+#     - r-rcolorbrewer
+#     - r-reshape2
+#     - r-scales
+#     - r-stringr
+#     # SV_CALLS_DEV
+#     # - r-zoo
+#     - r-r.utils
+#     - r-ggnewscale
+#     # HEATMAP
+#     - r-tidyr
+#     # ARBIGENT
+#     - r-reshape
+#     - r-optparse
+#     - r-tidyr
+#     - r-ggbeeswarm
+#     - r-pheatmap
+#     # GC_correction
+#     - r-ggpubr
+#     - bioconductor-edger
+#     # SOLVE R lib issue
+#     - r-stringi=1.7.12
+#     # breakpointr
+#     - bioconductor-breakpointr
+RUN mkdir -p /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33
+COPY workflow/envs/rtools.yaml /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/scNOVA/scNOVA_DL.yaml
+#   prefix: /conda-envs/667f8c581ac0b8e1ef11912ad74bf264
+#   name: scNOVA_DL
+#   channels:
+#     - conda-forge
+#     - anaconda
+#   dependencies:
+#     - tensorflow=1.15.0
+#     - scikit-learn=0.21.3
+#     - python=3.7.4
+#     - matplotlib=3.1.1
+#     - pandas=0.25.3
+#     - h5py=2.10.0
+#     - numpy
+#     # scNOVA archive
+#     - unzip
+#     # Fix
+#     - pip:
+#         - cffi
+RUN mkdir -p /conda-envs/667f8c581ac0b8e1ef11912ad74bf264
+COPY workflow/envs/scNOVA/scNOVA_DL.yaml /conda-envs/667f8c581ac0b8e1ef11912ad74bf264/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/scNOVA/scNOVA_R.yaml
+#   prefix: /conda-envs/193f60d48796dd17eb847ea689b863a9
+#   name: scNOVA
+#   channels:
+#     - bioconda
+#     - conda-forge
+#     - r
+#   dependencies:
+#     - bioconductor-deseq2=1.30.0
+#     - r-matrixstats=0.58.0
+#     - r-pheatmap=1.0.12
+#     - r-gplots=3.1.1
+#     - r-umap=0.2.7.0
+#     - r-rtsne=0.15
+#     - r-factoextra=1.0.7
+#     - r-pracma=2.3.3
+#     - bioconductor-chromvar=1.12.0
+#     - r-nabor=0.5.0
+#     - bioconductor-motifmatchr=1.12.0
+#     - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.3
+#     - bioconductor-jaspar2016=1.18.0
+#     - r-codetools=0.2_18
+#     - r-fitdistrplus
+#     - r-doparallel
+#     - r-foreach
+RUN mkdir -p /conda-envs/193f60d48796dd17eb847ea689b863a9
+COPY workflow/envs/scNOVA/scNOVA_R.yaml /conda-envs/193f60d48796dd17eb847ea689b863a9/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml
+#   prefix: /conda-envs/ca9641251a8cb0057003875ad776c49f
+#   name: scNOVA_bioinfo_tools
+#   channels:
+#     - conda-forge
+#     - bioconda
+#     - anaconda
+#   dependencies:
+#     - samtools
+#     - biobambam
+#     - bedtools
+RUN mkdir -p /conda-envs/ca9641251a8cb0057003875ad776c49f
+COPY workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml /conda-envs/ca9641251a8cb0057003875ad776c49f/environment.yaml
+
+# Step 2: Generate conda environments
+
+RUN mamba env create --prefix /conda-envs/eba7cf011bffb12bcf25d066f6955913 --file /conda-envs/eba7cf011bffb12bcf25d066f6955913/environment.yaml && \
+    mamba env create --prefix /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 --file /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml && \
+    mamba env create --prefix /conda-envs/5681728a49bd83ceed09ba194330c858 --file /conda-envs/5681728a49bd83ceed09ba194330c858/environment.yaml && \
+    mamba env create --prefix /conda-envs/08d4368302a4bdf7eda6b536495efe7d --file /conda-envs/08d4368302a4bdf7eda6b536495efe7d/environment.yaml && \
+    mamba env create --prefix /conda-envs/13317d3185b8c4c0305fe98c6a708486 --file /conda-envs/13317d3185b8c4c0305fe98c6a708486/environment.yaml && \
+    mamba env create --prefix /conda-envs/f251d84cdc9f25d0e14b48e780261d66 --file /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml && \
+    mamba env create --prefix /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33 --file /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33/environment.yaml && \
+    mamba env create --prefix /conda-envs/667f8c581ac0b8e1ef11912ad74bf264 --file /conda-envs/667f8c581ac0b8e1ef11912ad74bf264/environment.yaml && \
+    mamba env create --prefix /conda-envs/193f60d48796dd17eb847ea689b863a9 --file /conda-envs/193f60d48796dd17eb847ea689b863a9/environment.yaml && \
+    mamba env create --prefix /conda-envs/ca9641251a8cb0057003875ad776c49f --file /conda-envs/ca9641251a8cb0057003875ad776c49f/environment.yaml && \
+    mamba clean --all -y
+# CUSTOM PART
+RUN wget https://zenodo.org/record/7697400/files/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz -P /workflow/data/ref_genomes/
+COPY /workflow/scripts/utils/install_R_package.R /conda-envs/
+RUN chmod -R 0777 /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33/lib/R/library && /conda-envs/20d80620cbddf1a1f6c1457dd1ad4a33/bin/Rscript /conda-envs/install_R_package.R /workflow/data/ref_genomes/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz