diff tool-data/destinations.py @ 0:b80ff7f43ad1 draft default tip

planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/destinations.py	Thu Sep 24 12:10:01 2015 -0400
@@ -0,0 +1,62 @@
+from galaxy.jobs import JobDestination
+import os
+import sys
+import json
+import cStringIO
+import logging
+
+log = logging.getLogger( __name__ )
+
+
+def dump(obj, nested_level=0, output=sys.stdout):
+    spacing = '   '
+    if type(obj) == dict:
+        print >> output, '%s{' % ((nested_level) * spacing)
+        for k, v in obj.items():
+            if hasattr(v, '__iter__'):
+                print >> output, '%s%s:' % ((nested_level + 1) * spacing, k)
+                dump(v, nested_level + 1, output)
+            else:
+                print >> output, '%s%s: %s' % ((nested_level + 1) * spacing, k, v)
+        print >> output, '%s}' % (nested_level * spacing)
+    elif type(obj) == list:
+        print >> output, '%s[' % ((nested_level) * spacing)
+        for v in obj:
+            if hasattr(v, '__iter__'):
+                dump(v, nested_level + 1, output)
+            else:
+                print >> output, '%s%s' % ((nested_level + 1) * spacing, v)
+        print >> output, '%s]' % ((nested_level) * spacing)
+    else:
+        print >> output, '%s%s' % (nested_level * spacing, obj)
+
+
+def dynamic_slurm_cluster_gatk(job, tool_id):
+    # Allocate extra time
+    inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
+    inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
+    inp_data.update( [ ( da.name, json.loads(da.value) ) for da in job.parameters ] )
+    out = cStringIO.StringIO()
+    dump(inp_data, 1, out)
+    log.debug(out.getvalue())
+    
+    nativeSpecs = '--nodes=1 --ntasks=1'
+    
+    # runner doesn't allow to specify --cpus-per-task
+    # thus the mem calculation gets messy with more than 1 node
+    # --> translate nt ==> nodes, nct ==> ntasks
+    
+    if 'cond_threads' not in inp_data:
+        return JobDestination(runner="slurm")
+    
+    if inp_data['cond_threads']['cond_threads_enabled'] == "True":
+        nNodes = int(inp_data['cond_threads']['nt'])
+        nCPU   = int(inp_data['cond_threads']['nct'])
+        nMEM   = int(inp_data['cond_threads']['mem'])
+        if nMEM > 0:
+            nativeSpecs = '--nodes=%d --ntasks=%d --mem=%d' % (nNodes, nCPU*nNodes, nMEM)
+        else:
+            nativeSpecs = '--nodes=%d --ntasks=%d' % (nNodes, nCPU*nNodes)
+        
+    return JobDestination(runner="slurm", params={"nativeSpecification": nativeSpecs})
+