diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 5e124f0b..1941f4b1 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.4.1.9001 +current_version = 1.4.1.9002 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\.(?P\d+))? diff --git a/.github/workflows/build_conda_recipes.yaml b/.github/workflows/build_conda_recipes.yaml index 8b88e1e5..a2e77277 100644 --- a/.github/workflows/build_conda_recipes.yaml +++ b/.github/workflows/build_conda_recipes.yaml @@ -5,13 +5,13 @@ on: branches: - master - bundle_update_2023 - - ensembl_v111 + - conda_deps env: atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} recipe_path: conda/recipe env_yml_path: conda/env/yml env_lock_path: conda/env/lock - VERSION: '1.4.1.9001' # versioned by bump2version + VERSION: '1.4.1.9002' # versioned by bump2version jobs: build_pcgrr_conda_pkg: # When merging to one of the branches above and the commit message matches @@ -30,7 +30,7 @@ jobs: environment-file: ${{ env.env_yml_path }}/condabuild.yml - name: 🐍 Conda pkg build and upload run: | - conda mambabuild ${recipe_path}/pcgrr -c conda-forge -c bioconda --token ${atoken} --quiet + conda mambabuild ${recipe_path}/pcgrr -c umccr -c conda-forge -c bioconda --token ${atoken} build_pcgr_conda_pkg: # When merging to one of the branches above and the commit message matches if: "startsWith(github.event.head_commit.message, 'Bump version:')" @@ -91,7 +91,7 @@ jobs: cp pcgrr/DESCRIPTION . # hack for pkgdown to work printf "pcgrr version:\n" Rscript -e "packageVersion('pcgrr')" - Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://sigven.github.io/pcgr/'), branch = 'gh-pages', new_process = FALSE)" + Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = 'Built PCGR website - see https://sigven.github.io/pcgr/', branch = 'gh-pages', new_process = FALSE)" docker_deploy: name: Build and deploy Docker @@ -131,9 +131,9 @@ jobs: with: ref: v${{ env.VERSION }} - name: 🏰 QEMU setup - uses: docker/setup-qemu-action@v2 + uses: docker/setup-qemu-action@v3 - name: 🏯 Buildx setup - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 - name: DockerHub login uses: docker/login-action@v3 with: diff --git a/conda/env/yml/pcgr.yml b/conda/env/yml/pcgr.yml index c53892bc..f3164cf0 100644 --- a/conda/env/yml/pcgr.yml +++ b/conda/env/yml/pcgr.yml @@ -6,7 +6,7 @@ channels: - conda-forge dependencies: - - pcgr::pcgr ==1.4.1.9001 # versioned by bump2version + - pcgr::pcgr ==1.4.1.9002 # versioned by bump2version - bedtools - bcftools - cyvcf2 diff --git a/conda/env/yml/pcgrr.yml b/conda/env/yml/pcgrr.yml index 4027beb6..39cfd0bd 100644 --- a/conda/env/yml/pcgrr.yml +++ b/conda/env/yml/pcgrr.yml @@ -7,7 +7,7 @@ channels: dependencies: - python - - pcgr::r-pcgrr ==1.4.1.9001 # versioned by bump2version + - pcgr::r-pcgrr ==1.4.1.9002 # versioned by bump2version - pcgr::r-cpsr - r-argparse - bioconductor-bsgenome.hsapiens.ucsc.hg38 diff --git a/conda/env/yml/pkgdown.yml b/conda/env/yml/pkgdown.yml index ca32bb14..15111068 100644 --- a/conda/env/yml/pkgdown.yml +++ b/conda/env/yml/pkgdown.yml @@ -4,7 +4,7 @@ channels: - bioconda - conda-forge dependencies: - - pcgr::r-pcgrr ==1.4.1.9001 # versioned by bump2version + - pcgr::r-pcgrr ==1.4.1.9002 # versioned by bump2version - r-pkgdown - r-readr - pandoc diff --git a/conda/recipe/pcgrr/build.sh b/conda/recipe/pcgrr/build.sh index a42a6a2f..52dc9bee 100644 --- a/conda/recipe/pcgrr/build.sh +++ b/conda/recipe/pcgrr/build.sh @@ -1,4 +1,7 @@ #!/bin/bash export DISABLE_AUTOBREW=1 +${R} -e "install.packages('devtools', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')" +${R} -e "install.packages('openxlsx2', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')" +${R} -e "devtools::install_github(repo = 'caravagnalab/CNAqc', ref = '274cde9', lib = '${PREFIX}/lib/R/library')" ${R} CMD INSTALL --build . ${R_ARGS} diff --git a/conda/recipe/pcgrr/meta.yaml b/conda/recipe/pcgrr/meta.yaml index 28611abc..b8afe1c4 100644 --- a/conda/recipe/pcgrr/meta.yaml +++ b/conda/recipe/pcgrr/meta.yaml @@ -1,6 +1,6 @@ package: name: r-pcgrr - version: 1.4.1.9001 # versioned by bump2version + version: 1.4.1.9002 # versioned by bump2version source: path: ../../../pcgrr @@ -19,85 +19,65 @@ requirements: - r-base ==4.2.3 - r-assertable - r-assertthat - - bioconductor-biocgenerics - - r-biocmanager - bioconductor-biostrings - - r-caret - - r-data.table - - r-devtools - - r-dt - r-dplyr + - r-dt - r-flexdashboard - - bioconductor-genomicranges + - r-formattable - bioconductor-genomeinfodb - r-ggplot2 - - r-ggpubr - r-glue - r-htmltools - - bioconductor-iranges - r-jsonlite - r-log4r - - r-magrittr - bioconductor-mutationalpatterns - r-plotly + - bioconductor-quantiseqr - r-quarto - quarto - - r-randomforest - - r-rcolorbrewer + - r-readr - r-reshape2 - r-rlang - r-rmarkdown - - r-roxygen2 - r-rrapply - bioconductor-s4vectors - r-scales - r-stringr + - r-stringi - r-tidyr - - r-upsetr - - r-usethis - - bioconductor-variantannotation + - r-yaml run: - r-base ==4.2.3 - r-assertable - r-assertthat - - bioconductor-biocgenerics - - r-biocmanager - bioconductor-biostrings - - r-caret - - r-data.table - - r-devtools - - r-dt - r-dplyr + - r-dt - r-flexdashboard - - bioconductor-genomicranges + - r-formattable - bioconductor-genomeinfodb - r-ggplot2 - - r-ggpubr - r-glue - r-htmltools - - bioconductor-iranges - r-jsonlite - r-log4r - - r-magrittr - bioconductor-mutationalpatterns - r-plotly + - bioconductor-quantiseqr - r-quarto - quarto - - r-randomforest - - r-rcolorbrewer + - r-readr - r-reshape2 - r-rlang - r-rmarkdown - - r-roxygen2 - r-rrapply - bioconductor-s4vectors - r-scales - r-stringr + - r-stringi - r-tidyr - - r-upsetr - - r-usethis - - bioconductor-variantannotation + - r-yaml test: commands: diff --git a/pcgr/_version.py b/pcgr/_version.py index b7004a16..9af07b84 100644 --- a/pcgr/_version.py +++ b/pcgr/_version.py @@ -1,2 +1,2 @@ # versioned by bump2version -__version__ = '1.4.1.9001' +__version__ = '1.4.1.9002' diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION index 37d74e99..a73cb620 100644 --- a/pcgrr/DESCRIPTION +++ b/pcgrr/DESCRIPTION @@ -1,7 +1,7 @@ Package: pcgrr Type: Package Title: Personal Cancer Genome ReporteR -Version: 1.4.1.9001 +Version: 1.4.1.9002 Date: 2024-04-21 Authors@R: c(person(given = "Sigve", @@ -27,16 +27,15 @@ biocViews: Remotes: caravagnalab/CNAqc Imports: - openxlsx2, - quantiseqr, - yaml, assertable, assertthat, Biostrings, CNAqc, DT, dplyr, + DT, flexdashboard, + formattable, GenomeInfoDb, ggplot2, glue, @@ -44,7 +43,9 @@ Imports: jsonlite, log4r, MutationalPatterns, + openxlsx2, plotly, + quantiseqr, quarto, readr, reshape2, @@ -52,14 +53,15 @@ Imports: rmarkdown, rrapply, S4Vectors, - formattable, scales, stringr, stringi, - tidyr + tidyr, + yaml Depends: R (>= 4.0) Suggests: + cpsr, testthat, devtools, BSgenome.Hsapiens.UCSC.hg19, diff --git a/pcgrr/R/data.R b/pcgrr/R/data.R index e0c4bd0e..ae296545 100644 --- a/pcgrr/R/data.R +++ b/pcgrr/R/data.R @@ -88,3 +88,8 @@ #' "color_palette" +#' TSV columns +"tsv_cols" + +#' DT Display +"dt_display" diff --git a/pcgrr/R/output_data.R b/pcgrr/R/output_data.R index a8477b57..d242f6de 100644 --- a/pcgrr/R/output_data.R +++ b/pcgrr/R/output_data.R @@ -134,7 +134,7 @@ get_excel_sheets <- function(report = NULL){ i <- 1 while(i <= 2){ tier_data <- - pcgrr:::get_dt_tables( + get_dt_tables( report = pcg_report, tier = i, variant_class = "cna") if(NROW(tier_data$by_eitem) > 0){ @@ -198,7 +198,7 @@ get_excel_sheets <- function(report = NULL){ i <- 1 while(i <= 2){ tier_data <- - pcgrr:::get_dt_tables( + get_dt_tables( report = pcg_report, tier = i, variant_class = "snv_indel") if(NROW(tier_data$by_eitem) > 0){ diff --git a/pcgrr/man/dt_display.Rd b/pcgrr/man/dt_display.Rd new file mode 100644 index 00000000..1fe37f3c --- /dev/null +++ b/pcgrr/man/dt_display.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{dt_display} +\alias{dt_display} +\title{DT Display} +\format{ +An object of class \code{list} of length 8. +} +\usage{ +dt_display +} +\description{ +DT Display +} +\keyword{datasets} diff --git a/pcgrr/man/tsv_cols.Rd b/pcgrr/man/tsv_cols.Rd new file mode 100644 index 00000000..2df63f46 --- /dev/null +++ b/pcgrr/man/tsv_cols.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{tsv_cols} +\alias{tsv_cols} +\title{TSV columns} +\format{ +An object of class \code{list} of length 2. +} +\usage{ +tsv_cols +} +\description{ +TSV columns +} +\keyword{datasets} diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd index ab9b59c9..ed1e3222 100644 --- a/pcgrr/vignettes/installation.Rmd +++ b/pcgrr/vignettes/installation.Rmd @@ -12,7 +12,7 @@ output: rmarkdown::html_document software requirements: ```bash -PCGR_VERSION="1.4.1.9001" +PCGR_VERSION="1.4.1.9002" PCGR_REPO="https://raw.githubusercontent.com/sigven/pcgr/v${PCGR_VERSION}/conda/env/lock/" PLATFORM="linux" # or "osx" @@ -79,7 +79,7 @@ Download and unpack the latest software release from