Added individual job yaml files.

chipathlon/db.py

+from pymongo import MongoClient
+
+def setup

chipathlon/jobs/bwa_align_paired.yaml

+bwa_align_paired:
+  inputs:
+    - fna
+    - fastq
+    - fastq
+  outputs:
+    - sam
+  arguments:
+    - "-M":
+      changeable: false
+      required: true
+      value: false
+    - "-t":
+      changeable: true
+      required: false
+      default: 1
+      value: true
+    - "$inputs.0":
+      changeable: false
+      required: true
+      value: false
+    - "$inputs.1":
+      changeable: false
+      required: true
+      value: false
+    - "$inputs.2":
+      changeable: false
+      required: true
+      value: false
+  walltime: 2000
+  memory: 2000

chipathlon/jobs/bwa_align_single.yaml

+bwa_align_single:
+  inputs:
+    - fna
+    - fastq
+  outputs:
+    - sai
+  command: bwa
+  arguments:
+    - aln:
+        changeable: false
+        required: true
+        value: false
+    - "-q":
+        changeable: true
+        required: false
+        default: 5
+        value: true
+    - "-l":
+        changeable: true
+        required: false
+        default: 32
+        value: true
+    - "-k":
+        changeable: true
+        required: false
+        default: 2
+        value: true
+    - "-t":
+        changeable: true
+        required: false
+        default: 1
+        value: true
+    - "$inputs.0":
+        changeable: false
+        required: true
+        value: false
+    - "$inputs.1":
+        changeable: false
+        required: true
+        value: false
+  walltime: 2000
+  memory: 2000

chipathlon/jobs/bwa_sai_to_sam.yaml

+bwa_sai_to_sam:
+  inputs:
+    - fna
+    - sai
+    - fastq
+  outputs:
+    - sam
+  command: bwa
+  arguments:
+    - samse:
+      changeable: false
+      required: true
+      value: false
+    - "$inputs.0":
+      changeable: false
+      required: true
+      value: false
+    - "$inputs.1":
+      changeable: false
+      required: true
+      value: false
+    - "$inputs.2":
+      changeable: false
+      required: true
+      value: false
+  walltime: 2000
+  memory: 2000

chipathlon/jobs/samtools_sam_to_bam.yaml

+samtools_sam_to_bam:
+  inputs:
+    - sam
+  outputs:
+    - bam
+  arguments:
+    - view:
+      changeable: false
+      required: true
+      value: false
+    - "-bS"
+      changeable: false
+      required: true
+      value: false
+    - "$inputs.0"
+      changeable: false
+      required: true
+      value: false
+  walltime: 2000
+  memory: 2000

chipathlon/utils.py

 import sys
 
-def progress(current, end):
+def progress(current, end, length = 20):
     percent = float(current) / end
-    hashes = "#" * int(round(percent * 20))
-    spaces = " " * (20 - len(hashes))
+    hashes = "#" * int(round(percent * length))
+    spaces = " " * (length - len(hashes))
     sys.stdout.write("\rProcessed %s / %s entries. [%s] %s%%" % (current, end, hashes + spaces, int(round(percent * 100))))
     sys.stdout.flush()