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uc-bd2k / GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator
https://shiny.ilincs.org/grein
GNU General Public License v2.0
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GEO_data_processing.R get error #16

Closed ngutrinh closed 3 years ago

ngutrinh commented 3 years ago

Hi, I try to run the GREP2 for the new dataset, I just follow the GEO_data_processing.R but get the error, In folder "data/user_geo_request/" I only saw the test.txt file with empty content. , how I can fix it? For example, I want to do with the dataset: GSE22666

library(GREP2)

logdir <- "data/user_geo_request/" destdir <- "data/user_geo_request/" cat(paste("STEP 1: Processing starts... ","\n",sep=""),file=paste0(logdir,"/",geo_series_acc,"/log.txt")) Error in paste0(logdir, "/", geo_series_acc, "/log.txt") : object 'geo_series_acc' not found

process_geo_rnaseq (geo_series_acc=GSE22666,destdir="data/user_geo_request", ascp=TRUE,prefetch_workspace="path_to_prefetch_workspace", ascp_path="path_to_aspera",get_sra_file=FALSE,trim_fastq=FALSE, trimmomatic_path=NULL,index_dir="path_to_indexDir", species=species,countsFromAbundance="lengthScaledTPM",n_thread=2) Error in process_geo_rnaseq(geo_series_acc = GSE22666, destdir = "data/user_geo_request", : unused arguments (get_sra_file = FALSE, trimmomatic_path = NULL)