Added node support. Updated database to load files in chunks.

chipathlon/jobs/scripts/sort_macs2.sh

 #!/bin/bash
 
-/bin/sort -k 8gr,8gr "$1" | awk 'BEGIN{OFS="\t"}{$r="PEAK_"NR; print $0;}' > "$2"
+/bin/sort -k 8gr,8gr "$1" | awk 'BEGIN{OFS="\t"}{$4="PEAK_"NR; print $0;}' > "$2"

chipathlon/tester.py

@@ -40,21 +40,27 @@ class InsertResultsTests(DatabaseTestCase):
         valid, msg, result_id = self.mdb.save_bed(
                                     "test/insert_tests/sample.bed",
                                     [],
-                                    ["ENCSR000BKT"],
+                                    ["ENCFF000RCB"],
                                     {"align_tool": "bowtie2", "read_end": "single"}
                                 )
-        self.result_ids.append(result_id)
+        if valid:
+            self.result_ids.append(result_id)
+        else:
+            print msg
         self.assertTrue(valid)
         return
 
     def test_insert_peak(self):
         valid, msg, result_id = self.mdb.save_peak(
                                     "test/insert_tests/sample.narrowPeak",
-                                    ["ENCSR000BLJ"],
-                                    ["ENCSR000BKT"],
+                                    ["ENCFF000RCB"],
+                                    ["ENCFF000RCB"],
                                     {"align_tool": "bwa", "read_end": "single", "peak_tool": "macs2"}
                                 )
-        self.result_ids.append(result_id)
+        if valid:
+            self.result_ids.append(result_id)
+        else:
+            print msg
         self.assertTrue(valid)
         return