Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/launcher/test/expFiles/expJobScriptTemplate.py @ 0:e0f8dcca02ed

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
1 #!/usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
3 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
4 import sys
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
5 import time
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
6 import shutil
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
7 from commons.core.checker.RepetException import RepetException
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
8 from commons.core.sql.TableJobAdaptator import TableJobAdaptator
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
9 from commons.core.sql.DbFactory import DbFactory
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
10 from commons.core.sql.Job import Job
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
11
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
12 try:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
13 newDir = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
14 print os.uname()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
15 beginTime = time.time()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
16 print 'beginTime=%f' % beginTime
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
17 print "work in dir '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
18 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
19 if not os.path.exists( "/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch" ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
20 raise IOError("ERROR: temporary directory '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch' doesn't exist")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
21
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
22 minFreeGigaInTmpDir = 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
23 freeSpace = os.statvfs("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
24 if ((freeSpace.f_bavail * freeSpace.f_frsize) / 1073741824.0 < minFreeGigaInTmpDir):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
25 raise RepetException("ERROR: less than %iG of input file in '/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch'" % minFreeGigaInTmpDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
26
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
27 os.chdir("/home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
28 newDir = "groupid_job1_20110505-105353"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
29 if os.path.exists(newDir):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
30 shutil.rmtree(newDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
31 os.mkdir(newDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
32 os.chdir(newDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
33
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
34 iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
35 iDb = DbFactory.createInstance()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
36 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
37 print "current status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
38 iTJA.changeJobStatus(iJob, "running")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
39 print "updated status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
40 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
41 iDb.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
42
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
43 log = os.system("touch dummyFile1")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
44 if log != 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
45 raise RepetException("ERROR: job returned %i" % log)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
46 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
47 print "job finished successfully"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
48 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
49 shutil.move("dummyFile1", "/home/user/workspace/repet_pipe/commons/core/launcher/test")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
50
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
51 os.chdir("..")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
52 shutil.rmtree(newDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
53
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
54 iDb = DbFactory.createInstance()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
55 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
56 print "current status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
57 iTJA.changeJobStatus(iJob, "finished")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
58 print "updated status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
59 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
60 iDb.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
61
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
62 endTime = time.time()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
63 print 'endTime=%f' % endTime
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
64 print 'executionTime=%f' % (endTime - beginTime)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
65 print os.uname()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
66 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
67
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
68 except IOError, e :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
69 print e
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
70 iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
71 iDb = DbFactory.createInstance()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
72 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
73 print "current status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
74 iTJA.changeJobStatus(iJob, "error")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
75 print "updated status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
76 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
77 iDb.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
78 sys.exit(1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
79
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
80 except Exception, e :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
81 print "tmpDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/dummyScratch"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
82 print "cDir is : /home/user/workspace/repet_pipe/commons/core/launcher/test/"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
83 print e
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
84 if newDir != None and os.path.exists("../%s" % newDir) and not os.path.exists("/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
85 os.chdir("..")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
86 shutil.move(newDir, "/home/user/workspace/repet_pipe/commons/core/launcher/test//%s" % newDir)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
87 iJob = Job(jobname = "job1", groupid = "groupid", launcherFile = "ClusterLauncher", node = os.getenv("HOSTNAME"))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
88 iDb = DbFactory.createInstance()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
89 iTJA = TableJobAdaptator(iDb, "dummyJobsTable")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
90 print "current status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
91 iTJA.changeJobStatus(iJob, "error")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
92 print "updated status: %s" % iTJA.getJobStatus(iJob)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
93 sys.stdout.flush()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
94 iDb.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
95 sys.exit(1)