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Bioconda.md

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Installation using the Bioconda environment

  1. Install MiniConda: In case you do not have Conda yet, it is easiest to just install MiniConda.

  2. Create environment:

    conda env create -n strandseqnation -f conda-environment.yml
source activate strandseqnation

    This includes prerequisites for R and Python scripts used in the pipeline

  3. Install mosaicatcher:

    Build using CMake.

    For optimal integration with mosaicatcher-pipeline version 1.0, please use version 47a06ed.

  4. Configure Snake.config.json

    Fill the config variables with the required file paths

    • mosaicatcher to the software installed in (iii)
    • reference to the reference genome FASTA file (requires an .fai index)
    • plot_script to the qc.R script contained within mosaicatcher (iii)
    • samtools, bcftools to the respective software

Note on how Conda environment was created

The provided environment conda-environment.yml is the result of running:

conda create -y -n strandseqnation snakemake=5.3 r-ggplot2=2.2 python bcftools bioconductor-biobase bioconductor-biocgenerics bioconductor-biocinstaller bioconductor-biocparallel bioconductor-biostrings bioconductor-bsgenome bioconductor-bsgenome.hsapiens.ucsc.hg38 bioconductor-delayedarray bioconductor-fastseg bioconductor-genomeinfodb bioconductor-genomeinfodbdata bioconductor-genomicalignments bioconductor-genomicranges bioconductor-iranges bioconductor-rsamtools bioconductor-rtracklayer bioconductor-s4vectors bioconductor-summarizedexperiment bioconductor-xvector bioconductor-zlibbioc htslib r-data.table r-peer samtools boost boost-cpp cairo certifi cmake pandas pango pip pixman python-dateutil r-assertthat r-base r-bh r-bitops r-colorspace r-cowplot r-curl r-devtools r-dichromat r-digest r-futile.logger r-futile.options r-git2r r-gridextra r-gtable r-hexbin r-httr r-jsonlite r-labeling r-lambda.r r-lattice r-lazyeval r-magrittr r-mass r-matrix r-matrixstats r-memoise r-mime r-munsell r-openssl r-plyr r-r6 r-rcolorbrewer r-rcpp r-rcurl r-reshape2 r-rlang r-rstudioapi r-scales r-snow r-stringi r-stringr r-tibble r-viridislite r-whisker r-withr r-xml setuptools  numpy r-dplyr scipy whatshap freebayes r-mc2d r-pheatmap bioconductor-complexheatmap r-gplots

conda env export > conda-environment.yml

This avoids some annoying version downgrades that sometimes happen when creating an environment incrementally.