Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_convert.py @ 35:259891fce7fd draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
author peterjc
date Wed, 09 Aug 2017 13:32:11 -0400
parents 0785a6537f3e
children cee8f9005e43
comparison
equal deleted inserted replaced
34:0785a6537f3e 35:259891fce7fd
20 from StringIO import StringIO as BytesIO 20 from StringIO import StringIO as BytesIO
21 21
22 # Do we need any PYTHONPATH magic? 22 # Do we need any PYTHONPATH magic?
23 from mira4_make_bam import depad 23 from mira4_make_bam import depad
24 24
25 WRAPPER_VER = "0.0.10" # Keep in sync with the XML file 25 WRAPPER_VER = "0.0.11" # Keep in sync with the XML file
26 26
27 27
28 def run(cmd): 28 def run(cmd):
29 # Avoid using shell=True when we call subprocess to ensure if the Python 29 # Avoid using shell=True when we call subprocess to ensure if the Python
30 # script is killed, so too is the child process. 30 # script is killed, so too is the child process.
108 out_bam = options.bam 108 out_bam = options.bam
109 out_fasta = options.fasta 109 out_fasta = options.fasta
110 out_ace = options.ace 110 out_ace = options.ace
111 out_cstats = options.cstats 111 out_cstats = options.cstats
112 112
113 try: 113 if "MIRA4" in os.environ:
114 mira_path = os.environ["MIRA4"] 114 mira_path = os.environ["MIRA4"]
115 except KeyError: 115 mira_convert = os.path.join(mira_path, "miraconvert")
116 sys.exit("Environment variable $MIRA4 not set") 116 if not os.path.isfile(mira_convert):
117 mira_convert = os.path.join(mira_path, "miraconvert") 117 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
118 if not os.path.isfile(mira_convert): 118 % (mira_convert, ", ".join(os.listdir(mira_path))))
119 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" 119 else:
120 % (mira_convert, ", ".join(os.listdir(mira_path)))) 120 sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
121 mira_path = None
122 mira_convert = "miraconvert"
121 123
122 mira_convert_ver = get_version(mira_convert) 124 mira_convert_ver = get_version(mira_convert)
123 if not mira_convert_ver.strip().startswith("4.0"): 125 if not mira_convert_ver.strip().startswith("4.0"):
124 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)) 126 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert))
125 if options.version: 127 if options.version: