fix bioconductor function deprecations

.github/workflows/python-package-conda.yml

@@ -25,6 +25,7 @@ jobs:
       run: |
         micromamba --version
         micromamba env list
+        micromamba list -n drop_test
 
 #    - name: Install dependencies
 #      run: mamba env update -f environment.yml

drop/__init__.py

@@ -5,4 +5,4 @@
 from . import demo
 
 
-__version__ = "1.6.0"
+__version__ = "1.6.1"

drop/cli.py

@@ -17,7 +17,7 @@
 
 @click.group(invoke_without_command=True)
 @click_log.simple_verbosity_option(logger)
-@click.version_option('1.6.0',prog_name='drop')
+@click.version_option("1.6.0", prog_name='drop')
 
 def main():
     ctx = click.get_current_context()

drop/modules/aberrant-expression-pipeline/Counting/countReads.R

@@ -26,6 +26,7 @@ suppressPackageStartupMessages({
   library(Rsamtools)
   library(BiocParallel)
   library(GenomicAlignments)
+  library(GenomeInfoDb)
 })
 
 # Get strand specific information from sample annotation

drop/modules/aberrant-splicing-pipeline/Counting/03_filter_expression_FraseR.R

@@ -24,6 +24,10 @@
 saveRDS(snakemake, snakemake@log$snakemake)
 source(snakemake@params$setup, echo=FALSE)
 
+suppressPackageStartupMessages({
+  library(GenomeInfoDb)
+})
+
 opts_chunk$set(fig.width=12, fig.height=8)
 
 # input

drop/modules/aberrant-splicing-pipeline/Counting/exportCounts.R

@@ -20,7 +20,10 @@
 saveRDS(snakemake, snakemake@log$snakemake)
 source(snakemake@params$setup, echo=FALSE)
 
-library(AnnotationDbi)
+suppressPackageStartupMessages({
+  library(AnnotationDbi)
+  library(GenomeInfoDb)
+})
 
 # 
 # input

drop/modules/aberrant-splicing-pipeline/FRASER/06_annotate_genes.R

@@ -25,7 +25,11 @@
 
 saveRDS(snakemake, snakemake@log$snakemake)
 source(snakemake@params$setup, echo=FALSE)
-library(AnnotationDbi)
+
+suppressPackageStartupMessages({
+  library(AnnotationDbi)
+  library(GenomeInfoDb)
+})
 
 annotation <- snakemake@wildcards$annotation
 dataset    <- snakemake@wildcards$dataset

drop/modules/aberrant-splicing-pipeline/config.R

@@ -14,7 +14,7 @@ suppressPackageStartupMessages({
     library(plotly)
     library(DelayedMatrixStats)
     library(FRASER)
-  library(rhdf5)
+    library(rhdf5)
 })
 
 

drop/modules/mae-pipeline/MAE/Results.R

@@ -37,6 +37,7 @@ suppressPackageStartupMessages({
   library(SummarizedExperiment)
   library(R.utils)
   library(dplyr)
+  library(GenomeInfoDb)
 })
 
 # Read annotation and convert into GRanges

drop/modules/mae-pipeline/QC/create_matrix_dna_rna_cor.R

@@ -24,6 +24,7 @@ suppressPackageStartupMessages({
   library(magrittr)
   library(BiocParallel)
   library(data.table)
+  library(GenomeInfoDb)
 })
 
 register(MulticoreParam(snakemake@threads))

drop/template/Scripts/Pipeline/preprocessGeneAnnotation.R

@@ -21,6 +21,8 @@ suppressPackageStartupMessages({
   library(data.table)
   library(rtracklayer)
   library(magrittr)
+  library(txdbmaker)
+  library(GenomeInfoDb)
 })
 
 ## Create txdb

environment.yml

@@ -1,18 +1,55 @@
 name: drop_test
+
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - python>=3.11
-  - r-base>=4.4
+  - python >=3.11
   - pip
-  - pandas>=3.0
-  - drop
-  - snakemake>=5,<8
-  - flake8
-  - bioconductor-bsgenome.hsapiens.ucsc.hg19
-  - wbuild>1.8.0
+  - pandas >=3.0
+  - Click >=7.0
+  - click-log
+  - python-dateutil
+
+  # snakemake/wbuild
+  - wbuild >=1.8=pyhdfd78af_2
+  - snakemake >=5.5.2,<8
+  - pandoc
+  - graphviz
+
+  # command line tools
+  - bc
+  - wget
+  - htslib
+  - samtools >=1.9
+  - bcftools >=1.9
+  - gatk4 >=4.0.4
+  - star >=2.7
+
+  # R dependencies
+  - r-base >=4.4
   - r-dt
+  - r-rmarkdown
+  - r-knitr
+  - r-ggplot2
+  - r-ggthemes
+  - r-cowplot
+  - r-data.table
+  - r-dplyr
+  - r-tidyr
+  - r-magrittr
+  - r-devtools
+  - r-tmae >=1.0.5
+
+  # bioconductor packages
+  - bioconductor-deseq2
+  - bioconductor-genomicscores
+  - bioconductor-outrider >=1.28
+  - bioconductor-fraser >=2.6
+  - bioconductor-variantannotation
 
-  # required for downloading R packages through github
+  # testing dependencies
+  - flake8
+  - bioconductor-bsgenome.hsapiens.ucsc.hg19
   - unzip

tests/full_test_run/full_kremer_test.sh

@@ -20,11 +20,10 @@ cd ${run_folder}
 
 # create test env first
 env_path=${TMP}/env/env-$(basename ${run_folder})
-mkdir -p env
-mamba create -y -p ${env_path} \
-    "drop>=1.5" "pandoc>=2.4" "r-base>=4.4" \
-    "python>=3.12" "pip>=26.0" "yq>=3.4" \
-    "pandas>=3.0"
+mkdir -p $(dirname ${env_path})
+wget "https://github.com/gagneurlab/drop/blob/${branch_name}/environment.yml"
+yq -r '.dependencies[] | strings' environment.yml > environment.txt
+mamba create -y -p ${env_path} --file ./environment.txt
 source $(dirname ${CONDA_EXE})/activate ${env_path}
 
 # Report locations in the end
@@ -35,12 +34,6 @@ trap report_folder_on_exit EXIT
 trap report_folder_on_exit INT
 
 
-# Install R data packages required for the pipeline
-Rscript -e "options(repos=structure(c(CRAN='https://cloud.r-project.org')), warn = -1); install.packages('BiocManager');"
-Rscript -e "BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')" &
-Rscript -e "BiocManager::install('MafDb.gnomAD.r2.1.hs37d5')" &
-wait
-
 # install version from git branch
 pip install --no-deps --force-reinstall \
     "git+https://github.com/gagneurlab/drop@${branch_name}"

tests/full_test_run/kremer_test.R

@@ -124,3 +124,5 @@ qc_match_anno <- sapply(seq_len(nrow(qc_matches)), function(x){
 stopifnot(qc_match_anno)
 
 
+# report success
+message("All checks passed!")