trinity: trinity_wrapper.py annotate

annotate trinity_wrapper.py @ 1:88ada07f855c draft

Adding align_and_estimate_abundance tool.

author	trinity_ctat
date	Thu, 21 Sep 2017 14:31:42 -0400
parents	f571ca145e9d
children

rev	line source
0 f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	1 #!/usr/bin/env python
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	2
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	3 '''
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	4 trinity_runner.py
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	5 This program is used as a wrapper for Trinity to allow an automatic rerun of failed jobs. It takes arguments for a typical Trinity run:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	6 ~ Required args ~
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	7 Input files - single or paired (left and right)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	8 File type (fasta, fastq)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	9 Max memory - this I need to derive somehow from the dynamic runner using Galaxy slots
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	10
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	11 ~ Optional args ~
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	12 Output directory - this allows users to run the same job over in case it walltime'd out or failed for recoverable reasons.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	13
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	14 --
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	15 Created Tuesday, 7 March 2017.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	16 Carrie Ganote
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	17
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	18 Licensed to Indiana University under Creative Commons 3.0
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	19 '''
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	20 import subprocess32
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	21 import argparse
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	22 import logging as log
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	23 import sys
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	24 import os
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	25 import errno
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	26 from datetime import datetime
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	27
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	28 TRINITY_OUT_DIR = "trinity_out_dir"
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	29
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	30 def main(*args):
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	31 parser = argparse.ArgumentParser(description="")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	32 parser.add_argument("-o","--output", help="Name of output directory")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	33 parser.add_argument("-q","--seqType", help="Type of reads; fa or fq")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	34 parser.add_argument("-m","--max_memory", help="How much memory to allocate? Or maybe how many cpus?")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	35 parser.add_argument("-p","--mem_per_cpu", help="Memory PER CPU, in GB, in case we want to multiply mem x cpu at runtime")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	36 parser.add_argument("-s","--single", help="Single read file input")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	37 parser.add_argument("-l","--left", help="Left read file from paired inputs")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	38 parser.add_argument("-r","--right", help="Right read file from paired inputs")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	39 parser.add_argument("-v","--verbose", help="Enable debugging messages to be displayed", action='store_true')
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	40 parser.add_argument("-g","--log", help="Log file")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	41 parser.add_argument("-t","--timing", help="Timing file, if it exists", default=None)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	42 parser.add_argument("-d","--dir", help="if supplying a rerunnable job, this is the (hopefully unique) name of the directory to run it in.")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	43 parser.add_argument("-u","--user", help="Username to run job under")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	44 parser.add_argument("-f","--fullpath", help="if supplying a rerunnable job, this is the full path (except the user and dir names) to run the job in.")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	45 parser.add_argument("-c","--CPU", help="CPUs, either a hard coded numer or from Galaxy slots")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	46 # parser.add_argument("-","--", help="")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	47 args = parser.parse_args()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	48
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	49 if args.verbose:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	50 log.basicConfig(format='%(message)s',level=log.DEBUG)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	51 cmd = ["Trinity"]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	52
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	53 ### Add rerun ability ###########################################
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	54 # This variable tells us later whether to copy the files back to the job working directory
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	55 copyback = False
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	56 if args.dir and args.user and args.fullpath:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	57 cleandir = args.dir
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	58 chars = "\\`*_{}[]()>#+-.!$&;\| "
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	59 for c in chars:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	60 if c in cleandir:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	61 cleandir = cleandir.replace(c, "_")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	62 rerunPath = "%s/%s/%s" % (args.fullpath, args.user, cleandir)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	63 print "Rerunpath is ",rerunPath
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	64 try:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	65 os.makedirs(rerunPath)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	66 print "Created dir ",rerunPath
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	67 except OSError as exc:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	68 if exc.errno == errno.EEXIST and os.path.isdir(rerunPath):
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	69 pass
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	70 else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	71 raise
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	72 copyback = os.getcwd()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	73 outdir = copyback + "/" + TRINITY_OUT_DIR
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	74 try:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	75 os.makedirs(outdir)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	76 print "Created dir ",outdir
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	77 except OSError as exc:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	78 if exc.errno == errno.EEXIST and os.path.isdir(outdir):
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	79 pass
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	80 else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	81 raise
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	82 os.chdir(rerunPath)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	83
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	84 ### Add information for reads ###################################
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	85 if args.left and args.right:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	86 cmd += ["--left",args.left,"--right", args.right]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	87 elif args.single:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	88 cmd += ["--single",args.single]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	89 else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	90 raise Exception ("Need input files in order to run Trinity!")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	91
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	92 ### Add seqtype ##################################################
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	93 if args.seqType:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	94 cmd += ["--seqType",args.seqType]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	95 else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	96 raise Exception ("Please specify a file type for your reads!")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	97
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	98 ### Memory and CPU management ####################################
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	99 if args.mem_per_cpu and not args.max_memory:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	100 if args.CPU:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	101 memry = int(args.CPU) * int(args.mem_per_cpu)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	102 memstr = "%dG" % (memry)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	103 cmd += ["--max_memory",memstr]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	104 else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	105 memry = 2 * int(args.mem_per_cpu)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	106 memstr = "%dG" % (memry)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	107 cmd += ["--max_memory",memstr]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	108 elif args.max_memory and not args.mem_per_cpu:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	109 cmd += ["--max_memory",args.max_memory]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	110 else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	111 raise Exception ("Please pick Memory per cpu, or max mem, but not both.")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	112 if args.CPU:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	113 cmd += ["--CPU", args.CPU]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	114
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	115 ### Enough args, let's run it ####################################
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	116 print "About to write to %s" % args.log
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	117 out = open(args.log, 'w')
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	118 totalattempts = attempts = 2
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	119 ec = 1
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	120 finish = 1
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	121 out.write("Command is:\n%s\n" % (" ".join(cmd)))
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	122
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	123 ### There is definitely some value in running the job more than once, especially if it dies for stupid reasons.. ###
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	124 while ec != 0 and attempts > 0 and finish != 0:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	125
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	126 dt = datetime.now()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	127 dtstr = dt.strftime("%d/%m/%y %H:%M")
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	128 out.write("Beginning attempt %d of Trinity job at %s\n" % (totalattempts - attempts +1, dtstr) )
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	129 attempts -= 1
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	130 ec = subprocess32.call(cmd, shell=False, stdin=None, stdout=out, stderr=out, timeout=None)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	131 out.write("Trinity exited with status %d\n" % ec)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	132
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	133 greplog = open("greplog", 'w')
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	134 cmds = ["grep", 'All commands completed successfully', args.log]
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	135 finish = subprocess32.call(cmds,shell=False, stdin=None, stdout=greplog, stderr=greplog, timeout=None)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	136 greplog.close()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	137 out.write("Finished and found the success command with grep code %d\n" % finish)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	138
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	139 if ec == 0 and args.timing is not None:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	140 if copyback is not False:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	141 cwd = os.getcwd()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	142 dest = copyback + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	143 src = cwd + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	144 print "copying trinity outputs from %s to %s" % (src, dest)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	145 os.symlink(src, dest)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	146
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	147 #copy the timing file into the log
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	148 try:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	149 handle = open (args.timing, 'r')
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	150 for line in handle:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	151 out.write(line)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	152 handle.close()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	153 except (OSError, IOError) as e:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	154 print "Oops, no timing file found? ",e
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	155
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	156
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	157 out.close()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	158 exit (ec)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	159
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	160 if __name__ == "__main__":
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	161 main(*sys.argv)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	162

Mercurial > repos > trinity_ctat > trinity

annotate trinity_wrapper.py @ 1:88ada07f855c draft