--- a/peptide_shaker.xml	Sat Apr 10 15:57:17 2021 +0000
+++ b/peptide_shaker.xml	Fri May 21 19:13:14 2021 +0000
@@ -26,8 +26,6 @@
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $bin_dir = "bin"
         #set $exporting_followup_boolean = False
-        ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
-        ## trap ">&2 cat resources/*.log" EXIT;
 
         mkdir output_reports &&
         cwd=`pwd` &&
@@ -70,10 +68,13 @@
         ######################
         ## PeptideShakerCLI ##
         ######################
+        
+        ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package).
+
         peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
             -gui 0
             -temp_folder \$cwd/PeptideShakerCLI
-            -log \$cwd/resources
+            -use_log_folder 0
             -reference '$exp_str'
             -identification_files \$cwd/searchgui_input.zip
             -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
@@ -187,7 +188,12 @@
                 #end if
             #end if
         #end if
-
+        
+        ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)"
+        ## is fixed , we can avoid the process to be stopped by removing that message from the output
+        
+        |   grep -v "resources/conf/paths.txt (Permission denied)"
+        
         ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
         #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
             ## This unzipping command creates a reports folder into the current folder!