diff --git a/singlecell/resources/chunks/RunConga.R b/singlecell/resources/chunks/RunConga.R index 12414779f..cd46d92dc 100644 --- a/singlecell/resources/chunks/RunConga.R +++ b/singlecell/resources/chunks/RunConga.R @@ -7,6 +7,34 @@ if (!file.exists(netRc)) { invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc)) Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder) +if (!reticulate::py_module_available(module = 'conga')) { + logger::log_warn('python conga not found!') + logger::log_warn(paste0('Python available: ', reticulate::py_available())) + logger::log_warn('Python config') + pyConfig <- reticulate::py_config() + for (pn in names(pyConfig)) { + logger::log_warn(paste0(pn, ': ', paste0(pyConfig[[pn]]), collapse = ',')) + } + + logger::log_warn(paste0('pythonpath: ', reticulate::py_config()$pythonpath)) + + logger::log_warn('Python packages:') + for (pn in reticulate::py_list_packages()$package) { + logger::log_warn(pn) + } + + if ('conga' %in% reticulate::py_list_packages()$package) { + tryCatch({ + logger::log_warn(reticulate::import('conga')) + }, error = function(e){ + logger::log_warn("Error with reticulate::import('conga')") + logger::log_warn(reticulate::py_last_error()) + logger::log_warn(conditionMessage(e)) + traceback() + }) + } +} + for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])