cpsr.R: export pcgrr conda env path + quarto evars

sigven · Jun 6, 2024 · b0827b2 · b0827b2
1 parent f8ec4fa
commit b0827b2
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/pcgr/cpsr.py b/pcgr/cpsr.py
@@ -310,13 +310,14 @@ def run_cpsr(conf_options, input_data, output_data):
 
         # export PATH to R conda env Rscript
         pcgrr_conda = conf_options['pcgrr_conda']
+        quarto_env_vars = utils.quarto_evars_path(pcgrr_conda)
         pcgr_conda = utils.conda_prefix_basename()
         rscript = utils.script_path(pcgrr_conda, 'bin/Rscript')
         cpsrr_script = utils.script_path(pcgr_conda, 'bin/cpsr.R')
-
+        export_pcgrr = utils.pcgrr_conda_env_export(pcgrr_conda)
         ## CPSR|writer - generate HTML report
         cpsr_report_command = (
-                 f"{rscript} {cpsrr_script} {yaml_fname}")
+                 f"{export_pcgrr} && {rscript} {cpsrr_script} {yaml_fname} {quarto_env_vars}")
 
         if debug:
             print(cpsr_report_command)

diff --git a/scripts/cpsr.R b/scripts/cpsr.R
@@ -11,6 +11,8 @@ suppressWarnings(suppressPackageStartupMessages(library(log4r)))
 ## YAML file produced by CPSR Python workflow
 ## - settings and paths to reference data and annotated input sample files
 yaml_fname <- as.character(args[1])
+quarto_evars_path <- as.character(args[2])
+pcgrr::export_quarto_evars(quarto_evars_path)
 
 my_log4r_layout <- function(level, ...) {
   paste0(format(Sys.time()), " - cpsr-report-generation - ",