1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
|
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
|
