Merge pull request #66 from ENCODE-DCC/PIP-120-different-spp-instances

Allow to specify an instance type for spp

dnanexus/call_chip_from_tas.py

@@ -73,6 +73,7 @@ def t_or_f(arg):
     # parser.add_argument('--idrversion', help="IDR version (relevant only if --idr is specified", default="2")
     parser.add_argument('--dryrun', help="Formulate the run command, but don't actually run", default=False, action='store_true')
     parser.add_argument('--spp_version', help="spp version", default="1.14")
+    parser.add_argument('--spp_instance', help="Override the spp applet instance type", default=None)
     parser.add_argument('--control', help="Use specified control tagAlign rather than infer one.", default=None)
     parser.add_argument('--accession', help="Accession the results to the ENCODE Portal", default=False, action='store_true')
     parser.add_argument('--fqcheck', help="If --accession, check that analysis is based on latest fastqs on ENCODEd", type=t_or_f, default=None)
@@ -705,10 +706,10 @@ def main():
                 '--rep2 %s' % (tas['rep2_ta'].get('file_id')),
                 '--ctl2 %s' % (tas['rep2_ta'].get('control_id')),
             ])
-
+        if args.spp_instance:
+            command_strings.append('--spp_instance %s' % str(args.spp_instance))
         if args.fragment_length:
             command_strings.append('--fragment_length %s' % str(args.fragment_length))
-
         if blacklist:
             command_strings.append('--blacklist "%s"' % (blacklist))
         if args.debug:

dnanexus/chip_workflow.py

@@ -229,6 +229,10 @@ def t_or_f(arg):
         '--spp_version',
         help="Version string for spp",
         default="1.14")
+    parser.add_argument(
+        '--spp_instance',
+        help="Override the spp applet instance type",
+        default=None)
     parser.add_argument(
         '--pipeline_version',
         help="Version string for ENCODE pipeline",
@@ -778,7 +782,8 @@ def main():
                         'rep2_paired_end': rep2_paired_end,
                         'as_file': dxpy.dxlink(resolve_file(args.narrowpeak_as)),
                         'idr_peaks': True,
-                        'spp_version': args.spp_version
+                        'spp_version': args.spp_version,
+                        'spp_instance': args.spp_instance
                         }
             if chrom_sizes:
                 peaks_stage_input_mapping.update({'chrom_sizes': chrom_sizes})

dnanexus/encode_spp/dxapp.json

@@ -95,9 +95,15 @@
         },
         {   
             "name": "fragment_length",
-            "label": "use this fragment length instead of the one calculated from xcor",
+            "label": "Use this fragment length instead of the one calculated from xcor",
             "class": "int",
             "optional": true
+        },
+        {   
+            "name": "spp_instance",
+            "label": "If provided this will over-ride the default instance type for all spp peak-calling jobs",
+            "class": "string",
+            "optional": true
         }
     ],
     "outputSpec": [

dnanexus/encode_spp/src/encode_spp.py

@@ -24,7 +24,7 @@
 
 def spp(experiment, control, xcor_scores, chrom_sizes, spp_version,
         bigbed=False, as_file=None, name="spp", prefix=None,
-        fragment_length=None):
+        fragment_length=None, spp_instance=None):
     spp_applet = \
         dxpy.find_one_data_object(
             classname='applet',
@@ -45,7 +45,14 @@ def spp(experiment, control, xcor_scores, chrom_sizes, spp_version,
         spp_input.update({"as_file": as_file})
     if prefix:
         spp_input.update({"prefix": prefix})
-    return spp_applet.run(spp_input, name=name)
+    spp_args = {
+        'name': name,
+    }
+    if spp_instance:
+        spp_args.update({
+            'instance_type': spp_instance
+        })
+    return spp_applet.run(spp_input, **spp_args)
 
 
 def xcor_only(tags, paired_end, spp_version, name='xcor_only'):
@@ -68,7 +75,7 @@ def xcor_only(tags, paired_end, spp_version, name='xcor_only'):
 def main(rep1_ta, ctl1_ta, rep1_xcor, rep1_paired_end,
          npeaks, nodups,  chrom_sizes, spp_version,
          rep2_ta=None, ctl2_ta=None, rep2_xcor=None, rep2_paired_end=None,
-         as_file=None, idr_peaks=False, fragment_length=None):
+         as_file=None, idr_peaks=False, fragment_length=None, spp_instance=None):
 
     rep1_ta_file = dxpy.DXFile(rep1_ta)
     dxpy.download_dxfile(rep1_ta_file.get_id(), rep1_ta_file.name)
@@ -190,7 +197,8 @@ def main(rep1_ta, ctl1_ta, rep1_xcor, rep1_paired_end,
     common_args = {
         'chrom_sizes': chrom_sizes,
         'spp_version': spp_version,
-        'as_file':     as_file
+        'as_file':     as_file,
+        'spp_instance': spp_instance
         }
     if fragment_length is not None:
         common_args.update({'fragment_length': fragment_length})