Description: adapt web-backend for command-line usage
 See debian/README.source
Author: Afif Elghraoui <afif@debian.org>
Forwarded: no
Last-Update: 2018-02-11
--- assemblytics.orig/bin/web_pipeline
+++ assemblytics/bin/web_pipeline
@@ -1,5 +1,5 @@
 #!/bin/bash
-USAGE="web_pipeline delta output_prefix unique_length_required min_size"
+USAGE="Assemblytics delta output_prefix unique_length_required min_size max_size"
 if [ -z "$1" ]
   then
     echo "ERROR in Assemblytics: No delta file given"
@@ -49,7 +49,7 @@
 >&2 echo Input delta file: $DELTA
 >&2 echo Output prefix: $OUTPUT_PREFIX
 
-LOG_FILE=${OUTPUT_PREFIX%/*}/progress.log
+LOG_FILE=/dev/stdout
 
 
 echo "${OUTPUT_PREFIX##*/}" >> $LOG_FILE
@@ -94,8 +94,6 @@
                 
                 ./bin/Assemblytics_summary.py -i $OUTPUT_PREFIX.Assemblytics_structural_variants.bed -min $MINIMUM_SIZE -max $MAXIMUM_SIZE > $OUTPUT_PREFIX.Assemblytics_structural_variants.summary
 
-                zip $OUTPUT_PREFIX.Assemblytics_results.zip $OUTPUT_PREFIX.Assemblytics*
-                head $OUTPUT_PREFIX.Assemblytics_structural_variants.bed | column -t > $OUTPUT_PREFIX.variant_preview.txt
 
                 if grep -q "Total" $OUTPUT_PREFIX.Assemblytics_structural_variants.summary; 
                 then