Introduction to the OikScrambling package

Introduction

This package contains a collection of vignettes to perform the analysis of pairwise genome alignments between Oikopleura genomes.

The core functions used here are maintained in our GenomicBreaks R package, which is fully documented at: https://oist.github.io/GenomicBreaks.

How to build this site

As some of the computations take time, we build the vignettes on OIST’s HPC cluster Deigo using the ?pkgdown::build_site function, in a Git clone in a subdirectory of the /flash filesystem.

singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "pkgdown::build_site(devel=TRUE, lazy=TRUE)"

How to install or update the necessary packages

OikScrambling and GenomicBreaks

Sometimes it is necessary to upgrade the OikScrambling package; this is done with:

singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server R CMD INSTALL .

And before, it may be needed to update GenomicBreaks or BreakpointsData:

singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "remotes::install_github('oist/GenomicBreaks', repos=BiocManager::repositories())"
singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "install.packages('BreakpointsData', repos='https://oist.github.io/plessy_oikgenomes_drat/')"

The trick is that the GenomicBreaks singularity images are hardcoded to install new packages in R/library/GBreaks_singularity, which bypasses the the problem that the images are read-only.

Command to recompute the BreakPoints.Rdata file

srun -pcompute -c8 --mem 300G --pty singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "pkgdown::build_article('LoadGenomicBreaks')"

Commands to rebuild the whole site.

srun -pcompute -c8 --mem 300G --pty singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "pkgdown::build_site(devel=TRUE, lazy=TRUE)"
srun -pcompute -c8 --mem 300G --pty singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "pkgdown::build_site()"

Data packages

BSgenome packages

We need the sequences of the studied genomes. They are provided in a drat repository: https://oist.github.io/plessy_oikgenomes_drat/.

Example command to install one Oikopleura BSgenome package if you do not yet have it:

singularity exec /apps/unit/BioinfoUgrp/Other/RStudio_server/2023.09.0-463/RStudio_server Rscript -e "install.packages('BSgenome.Oidioi.OIST.OKI2018.I69', repos='https://oist.github.io/plessy_oikgenomes_drat/')"

Genome annotations

The annotations from /bucket/LuscombeU/common/Breakpoints/Annotations are distributed in the same drat repository as the alignment data.

install.packages('BreakpointsData', repos='https://oist.github.io/plessy_oikgenomes_drat/')

Charles Plessy