less verbose download

tools/dada2_assign_taxonomy/dada2_assign_taxonomy.script.R

@@ -50,19 +50,22 @@ library(yaml)
 yamlfile = paste0(Taxonomypath, "/info.yaml")
 taxURL = read_yaml(yamlfile)$train_set
 #http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/COI/BOLD_COI-5P/BOLD_COI-5P_022019.tar.gz to BOLD_COI-5P_022019.tar.gz
-frogsfile = paste0(Taxonomypath, basename(taxURL))
+frogsfile = paste0(Taxonomypath,"/", basename(taxURL))
 marker = gsub(".tar.gz",  "",  basename(taxURL))
 taxfile = paste0(Taxonomypath, "/train_set_",marker,".fa.gz")
 speciesfile = paste0(Taxonomypath, "/assignment_",marker,".fa.gz")
 
 if ( ! file.exists(taxfile))
 {  
-    download.file(taxURL, frogsfile, "wget")
-    cmd = paste0("cd ",Taxonomypath," && tar -xzf ",frogsfile," && rm -f ", frogsfile);
+    print(paste0("downloading Frogs trained dataset from :", taxURL))
+    download.file(taxURL, frogsfile, "wget", quiet = TRUE)
+    cmd = paste0("cd ",Taxonomypath," && tar -xzf ",frogsfile)
     system(cmd)
     unzipedDir = gsub(".tar.gz", "",  frogsfile)
-    
+    unlink(frogsfile);
+    print("converting to dada2 compatible format")
     MBBmakeTaxonomyFasta_RDP(paste0(unzipedDir, "/",marker,".fasta"), paste0(unzipedDir, "/",marker,".tax"), taxfile, compress=TRUE) 
+
     unlink(unzipedDir, recursive = TRUE, force = TRUE)
 
     speciesURL = read_yaml(yamlfile)$species_assignment