remove CPSR dependency

Merge branch 'bundle_update_2023' of github.com:sigven/pcgr into bundle_update_2023

# Conflicts:
#	pcgrr/DESCRIPTION

.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<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?

.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:

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

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

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

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}

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:

pcgr/_version.py

@@ -1,2 +1,2 @@
 # versioned by bump2version
-__version__ = '1.4.1.9001'
+__version__ = '1.4.1.9002'

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",
@@ -27,39 +27,41 @@ biocViews:
 Remotes:
     caravagnalab/CNAqc
 Imports:
-    openxlsx2,
-    quantiseqr,
-    yaml,
     assertable,
     assertthat,
     Biostrings,
     CNAqc,
     DT,
     dplyr,
+    DT,
     flexdashboard,
+    formattable,
     GenomeInfoDb,
     ggplot2,
     glue,
     htmltools,
     jsonlite,
     log4r,
     MutationalPatterns,
+    openxlsx2,
     plotly,
+    quantiseqr,
     quarto,
     readr,
     reshape2,
     rlang,
     rmarkdown,
     rrapply,
     S4Vectors,
-    formattable,
     scales,
     stringr,
     stringi,
-    tidyr
+    tidyr,
+    yaml
 Depends:
     R (>= 4.0)
 Suggests:
+    cpsr,
     testthat,
     devtools,
     BSgenome.Hsapiens.UCSC.hg19,

pcgrr/R/data.R

@@ -88,3 +88,8 @@
 #'
 "color_palette"
 
+#' TSV columns
+"tsv_cols"
+
+#' DT Display
+"dt_display"

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){

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 <https://github.com/sigven/
 Alternatively if you have `git` installed, you can do:
 
 ```bash
-PCGR_VERSION="1.4.1.9001"
+PCGR_VERSION="1.4.1.9002"
 OUTPUT_DIRECTORY="PCGR"
 
 git clone \
@@ -235,7 +235,7 @@ docker container run -it --rm \
     -v /Users/you/dir1/data:/root/pcgr_data \
     -v /Users/you/dir2/pcgr_inputs:/root/pcgr_inputs \
     -v /Users/you/dir3/pcgr_outputs:/root/pcgr_outputs \
-    sigven/pcgr:1.4.1.9001 \
+    sigven/pcgr:1.4.1.9002 \
     pcgr \
       --input_vcf "/root/pcgr_inputs/tumor_sample.BRCA.vcf.gz" \
       --pcgr_dir "/root/pcgr_data" \

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pcgr"
-version = "1.4.1.9001" # versioned by bump2version
+version = "1.4.1.9002" # versioned by bump2version
 description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine"
 authors = [
     {name = "Sigve Nakken", email = "[email protected]"},