Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4/mira4.py @ 7:902f01c1084b draft

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Uploaded v0.0.1 preview 7, with mirabait wrapper
author peterjc
date Fri, 25 Oct 2013 07:18:38 -0400
parents ffefb87bd414
children 302d13490b23
comparison
equal deleted inserted replaced
6:626d5cfd01aa 7:902f01c1084b
29 ver, tmp = child.communicate() 29 ver, tmp = child.communicate()
30 del child 30 del child
31 return ver.split("\n", 1)[0] 31 return ver.split("\n", 1)[0]
32 32
33 33
34 os.environ["PATH"] = "/mnt/galaxy/downloads/mira_4.0rc4_linux-gnu_x86_64_static/bin/:%s" % os.environ["PATH"] 34 try:
35 mira_binary = "mira" 35 mira_path = os.environ["MIRA4"]
36 except ImportError:
37 stop_err("Environment variable $MIRA4 not set")
38 mira_binary = os.path.join(mira_path, "mira")
39 if not os.path.isfile(mira_binary):
40 stop_err("Missing mira under $MIRA4, %r" % mira_binary)
41
36 mira_ver = get_version(mira_binary) 42 mira_ver = get_version(mira_binary)
37 if not mira_ver.strip().startswith("4.0"): 43 if not mira_ver.strip().startswith("4.0"):
38 stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver) 44 stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
39 if "-v" in sys.argv or "--version" in sys.argv: 45 if "-v" in sys.argv or "--version" in sys.argv:
40 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER) 46 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
41 sys.exit(0) 47 sys.exit(0)
42 48
49 def fix_threads(manifest):
50 """Tweak the manifest to alter the number of threads."""
51 try:
52 threads = int(os.environ.get("GALAXY_SLOTS", "1"))
53 except ValueError:
54 threads = 1
55 assert 1 <= threads
56 if threads == 1:
57 #Nothing to do...
58 return
59
60 handle = open(manifest)
61 text = handle.read()
62 handle.close()
63
64 text = text.replace(" -GE:not=1 ", " -GE:not=%i " % threads)
65
66 handle = open(manifest, "w")
67 handle.write(text)
68 handle.flush()
69 handle.close()
43 70
44 def log_manifest(manifest): 71 def log_manifest(manifest):
45 """Write the manifest file to stderr.""" 72 """Write the manifest file to stderr."""
46 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60)) 73 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
47 with open(manifest) as h: 74 with open(manifest) as h:
99 #/opt/galaxy-dist/database/job_working_directory/846/ 126 #/opt/galaxy-dist/database/job_working_directory/846/
100 temp = "." 127 temp = "."
101 #name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8] 128 #name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
102 name = "MIRA" 129 name = "MIRA"
103 manifest, out_maf, out_fasta, out_log = sys.argv[1:5] 130 manifest, out_maf, out_fasta, out_log = sys.argv[1:5]
131
132 fix_threads(manifest)
104 133
105 start_time = time.time() 134 start_time = time.time()
106 #cmd_list =sys.argv[8:] 135 #cmd_list =sys.argv[8:]
107 cmd_list = [mira_binary, manifest] 136 cmd_list = [mira_binary, manifest]
108 cmd = " ".join(cmd_list) 137 cmd = " ".join(cmd_list)