Merge pull request #67 from friendsofstrandseq/weber8thomas/clean-con…

…da-envs

Weber8thomas/clean conda envs

config/config.yaml

@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.3.4
+version: 2.3.5
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.3.4
+ashleys_pipeline_version: 2.3.5
 
 # Email for notifications about the pipeline's status
 email: ""

github-actions-runner/Dockerfile-2.3.5.dockerfile

@@ -0,0 +1,255 @@
+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="72e8bd41499b7a00b23bf8b7611bc709b4cf39ef9dda6af310328b74cc86321b"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_base.yaml
+#   prefix: /conda-envs/32c736a65a401b33605acfa7a0241299
+#   name: ashleys_base
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - ashleys-qc
+#     - bwa
+#     - mosaicatcher
+#     - multiqc
+#     - pandas
+#     - python=3.10
+#     - pysam
+#     - rsync
+#     - sambamba
+#     - samtools
+#     - scikit-learn=1.2.2
+#     - tabix
+RUN mkdir -p /conda-envs/32c736a65a401b33605acfa7a0241299
+ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_base.yaml /conda-envs/32c736a65a401b33605acfa7a0241299/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_rtools.yaml
+#   prefix: /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0
+#   name: rtools
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - bioconductor-edger
+#     - bioconductor-genomicranges
+#     - fonts-conda-forge
+#     - r-assertthat
+#     - r-base
+#     - r-cairo
+#     - r-cowplot
+#     - r-data.table
+#     - r-dplyr
+#     - r-ggplot2
+#     - r-ggpubr
+#     - r-platetools
+#     - r-r.utils
+#     - r-rcolorbrewer
+#     - r-reshape2
+#     - r-scales
+#     - r-stringi=1.7.12
+#     - r-tidyr
+#     - r-viridis
+RUN mkdir -p /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0
+ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_rtools.yaml /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0/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/e5cbb476a12203f97f2a0bb44963061d
+#   name: mc-base
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - intervaltree
+#     - matplotlib
+#     - pandas
+#     - parmap
+#     - perl
+#     - pybigwig
+#     - pypdf2
+#     - pysam
+#     - pytables
+#     - pyyaml
+#     - samtools
+#     - scipy
+#     - seaborn
+#     - tqdm
+#     - xopen
+RUN mkdir -p /conda-envs/e5cbb476a12203f97f2a0bb44963061d
+COPY workflow/envs/mc_base.yaml /conda-envs/e5cbb476a12203f97f2a0bb44963061d/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/905757e298f80370141afb02667ced2e
+#   name: rtools
+#   channels:
+#     - bioconda
+#     - conda-forge
+#   dependencies:
+#     - bioconductor-biocparallel
+#     - bioconductor-breakpointr
+#     - bioconductor-bsgenome
+#     - bioconductor-bsgenome.hsapiens.ucsc.hg38
+#     - bioconductor-complexheatmap
+#     - bioconductor-edger
+#     - bioconductor-genomicalignments
+#     - bioconductor-genomicranges
+#     - bioconductor-rsamtools
+#     - fonts-conda-forge
+#     - r-assertthat
+#     - r-base
+#     - r-biocmanager
+#     - r-cairo
+#     - r-cowplot
+#     - r-data.table
+#     - r-devtools
+#     - r-doparallel
+#     - r-dplyr
+#     - r-foreach
+#     - r-ggbeeswarm
+#     - r-ggnewscale
+#     - r-ggplot2
+#     - r-ggpubr
+#     - r-gplots
+#     - r-gtools
+#     - r-mc2d
+#     - r-optparse
+#     - r-pheatmap
+#     - r-r.utils
+#     - r-rcolorbrewer
+#     - r-reshape
+#     - r-reshape2
+#     - r-scales
+#     - r-stringi=1.7.12
+#     - r-stringr
+#     - r-tidyr
+#     - r-tidyr
+#     - strandphaser
+RUN mkdir -p /conda-envs/905757e298f80370141afb02667ced2e
+COPY workflow/envs/rtools.yaml /conda-envs/905757e298f80370141afb02667ced2e/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/scNOVA/scNOVA_DL.yaml
+#   prefix: /conda-envs/fdeedf32561210c2a9762946a26b4cca
+#   name: scNOVA_DL
+#   channels:
+#     - conda-forge
+#   dependencies:
+#     - h5py=2.10.0
+#     - matplotlib=3.1.1
+#     - numpy
+#     - pandas=0.25.3
+#     - python=3.7.4
+#     - scikit-learn=0.21.3
+#     - tensorflow=1.15.0
+#     - unzip
+#     - pip:
+#         - cffi
+RUN mkdir -p /conda-envs/fdeedf32561210c2a9762946a26b4cca
+COPY workflow/envs/scNOVA/scNOVA_DL.yaml /conda-envs/fdeedf32561210c2a9762946a26b4cca/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/scNOVA/scNOVA_R.yaml
+#   prefix: /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716
+#   name: scNOVA
+#   channels:
+#     - bioconda
+#     - conda-forge
+#   dependencies:
+#     - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.3
+#     - bioconductor-chromvar=1.12.0
+#     - bioconductor-deseq2=1.30.0
+#     - bioconductor-jaspar2016=1.18.0
+#     - bioconductor-motifmatchr=1.12.0
+#     - r-codetools=0.2_18
+#     - r-doparallel
+#     - r-factoextra=1.0.7
+#     - r-fitdistrplus
+#     - r-foreach
+#     - r-gplots=3.1.1
+#     - r-matrixstats=0.58.0
+#     - r-nabor=0.5.0
+#     - r-pheatmap=1.0.12
+#     - r-pracma=2.3.3
+#     - r-rtsne=0.15
+#     - r-umap=0.2.7.0
+RUN mkdir -p /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716
+COPY workflow/envs/scNOVA/scNOVA_R.yaml /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml
+#   prefix: /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e
+#   name: scNOVA_bioinfo_tools
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - bedtools
+#     - biobambam
+#     - samtools
+RUN mkdir -p /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e
+COPY workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e/environment.yaml
+
+# Step 2: Generate conda environments
+
+RUN mamba env create --prefix /conda-envs/32c736a65a401b33605acfa7a0241299 --file /conda-envs/32c736a65a401b33605acfa7a0241299/environment.yaml && \
+    mamba env create --prefix /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0 --file /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0/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/e5cbb476a12203f97f2a0bb44963061d --file /conda-envs/e5cbb476a12203f97f2a0bb44963061d/environment.yaml && \
+    mamba env create --prefix /conda-envs/f251d84cdc9f25d0e14b48e780261d66 --file /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml && \
+    mamba env create --prefix /conda-envs/905757e298f80370141afb02667ced2e --file /conda-envs/905757e298f80370141afb02667ced2e/environment.yaml && \
+    mamba env create --prefix /conda-envs/fdeedf32561210c2a9762946a26b4cca --file /conda-envs/fdeedf32561210c2a9762946a26b4cca/environment.yaml && \
+    mamba env create --prefix /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716 --file /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716/environment.yaml && \
+    mamba env create --prefix /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e --file /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e/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/905757e298f80370141afb02667ced2e/lib/R/library && /conda-envs/905757e298f80370141afb02667ced2e/bin/Rscript /conda-envs/install_R_package.R /workflow/data/ref_genomes/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz

workflow/envs/mc_base.yaml

@@ -3,22 +3,18 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - pandas
   - intervaltree
-  - scipy
-  - pysam
-  - tqdm
+  - matplotlib
+  - pandas
+  - parmap
   - perl
+  - pybigwig
   - pypdf2
-  - parmap
-  # NEW
+  - pysam
+  - pytables
   - pyyaml
-  - seaborn
-  - matplotlib
-  # SOLVE se-pe detection
   - samtools
-  # ArbiGent Hufsah deps
-  - pytables
+  - scipy
+  - seaborn
+  - tqdm
   - xopen
-  # Fix jbrowse tracks generation
-  - pybigwig

workflow/envs/rtools.yaml

@@ -2,22 +2,17 @@ name: rtools
 channels:
   - bioconda
   - conda-forge
-  - r
-  - anaconda
 dependencies:
-  # # NEW
-  - strandphaser
-  # ###############
   - bioconductor-biocparallel
+  - bioconductor-breakpointr
   - bioconductor-bsgenome
   - bioconductor-bsgenome.hsapiens.ucsc.hg38
   - bioconductor-complexheatmap
-  # - bioconductor-fastseg
+  - bioconductor-edger
   - bioconductor-genomicalignments
   - bioconductor-genomicranges
   - bioconductor-rsamtools
-  # - bioconductor-s4vectors
-  - fonts-anaconda
+  - fonts-conda-forge
   - r-assertthat
   - r-base
   - r-biocmanager
@@ -28,30 +23,22 @@ dependencies:
   - r-doparallel
   - r-dplyr
   - r-foreach
+  - r-ggbeeswarm
+  - r-ggnewscale
   - r-ggplot2
+  - r-ggpubr
   - r-gplots
   - r-gtools
   - r-mc2d
+  - r-optparse
+  - r-pheatmap
+  - r-r.utils
   - r-rcolorbrewer
+  - r-reshape
   - r-reshape2
   - r-scales
+  - r-stringi=1.7.12
   - 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
+  - strandphaser