Mercurial > repos > avowinkel > gatk
annotate 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
author | avowinkel |
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date | Thu, 24 Sep 2015 12:10:01 -0400 |
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b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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1 from galaxy.jobs import JobDestination |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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2 import os |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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3 import sys |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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4 import json |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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5 import cStringIO |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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6 import logging |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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7 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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8 log = logging.getLogger( __name__ ) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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9 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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10 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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11 def dump(obj, nested_level=0, output=sys.stdout): |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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12 spacing = ' ' |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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13 if type(obj) == dict: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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14 print >> output, '%s{' % ((nested_level) * spacing) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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15 for k, v in obj.items(): |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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16 if hasattr(v, '__iter__'): |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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17 print >> output, '%s%s:' % ((nested_level + 1) * spacing, k) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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18 dump(v, nested_level + 1, output) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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19 else: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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20 print >> output, '%s%s: %s' % ((nested_level + 1) * spacing, k, v) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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21 print >> output, '%s}' % (nested_level * spacing) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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22 elif type(obj) == list: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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23 print >> output, '%s[' % ((nested_level) * spacing) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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24 for v in obj: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
changeset
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25 if hasattr(v, '__iter__'): |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
changeset
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26 dump(v, nested_level + 1, output) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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27 else: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
changeset
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28 print >> output, '%s%s' % ((nested_level + 1) * spacing, v) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
changeset
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29 print >> output, '%s]' % ((nested_level) * spacing) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
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30 else: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
changeset
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31 print >> output, '%s%s' % (nested_level * spacing, obj) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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32 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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33 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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34 def dynamic_slurm_cluster_gatk(job, tool_id): |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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35 # Allocate extra time |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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36 inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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37 inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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38 inp_data.update( [ ( da.name, json.loads(da.value) ) for da in job.parameters ] ) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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39 out = cStringIO.StringIO() |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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40 dump(inp_data, 1, out) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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41 log.debug(out.getvalue()) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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42 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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43 nativeSpecs = '--nodes=1 --ntasks=1' |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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44 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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45 # runner doesn't allow to specify --cpus-per-task |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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46 # thus the mem calculation gets messy with more than 1 node |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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47 # --> translate nt ==> nodes, nct ==> ntasks |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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48 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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49 if 'cond_threads' not in inp_data: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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50 return JobDestination(runner="slurm") |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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51 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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52 if inp_data['cond_threads']['cond_threads_enabled'] == "True": |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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53 nNodes = int(inp_data['cond_threads']['nt']) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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54 nCPU = int(inp_data['cond_threads']['nct']) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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55 nMEM = int(inp_data['cond_threads']['mem']) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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56 if nMEM > 0: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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57 nativeSpecs = '--nodes=%d --ntasks=%d --mem=%d' % (nNodes, nCPU*nNodes, nMEM) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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58 else: |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
diff
changeset
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59 nativeSpecs = '--nodes=%d --ntasks=%d' % (nNodes, nCPU*nNodes) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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60 |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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61 return JobDestination(runner="slurm", params={"nativeSpecification": nativeSpecs}) |
b80ff7f43ad1
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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62 |