Mercurial > repos > fubar > differential_count_models

annotate rgToolFactory.py @ 50:60aceade5350 draft

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removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
author fubar
date Mon, 23 Dec 2013 21:36:34 -0500
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1 # rgToolFactory.py
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2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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9 #
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10 # august 2013
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11 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
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12 #
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13 # july 2013
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14 # added ability to combine images and individual log files into html output
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15 # Needs proper yaml control file but for now for each section you want separated out in the
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16 # HTML page, you need to use a name like foo or bar or header - they will be presented in alphabetic order
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17 #
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18 # Iff there's a log file foo.log and it will be layed out as preformated text in the HTML output
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19 # together with all images named like "foo_*.pdf in a separate "foo" section of the document
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20 # otherwise old format for html
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21 #
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22 # January 2013
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23 # problem pointed out by Carlos Borroto
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24 # added escaping for <>$ - thought I did that ages ago...
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25 #
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26 # August 11 2012
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27 # changed to use shell=False and cl as a sequence
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28
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29 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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30 # It also serves as the wrapper for the new tool.
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31 #
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32 # you paste and run your script
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33 # Only works for simple scripts that read one input from the history.
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34 # Optionally can write one new history dataset,
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35 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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36
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37 # DO NOT install on a public or important site - please.
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38
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39 # installed generated tools are fine if the script is safe.
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40 # They just run normally and their user cannot do anything unusually insecure
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41 # but please, practice safe toolshed.
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42 # Read the fucking code before you install any tool
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43 # especially this one
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44
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45 # After you get the script working on some test data, you can
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46 # optionally generate a toolshed compatible gzip file
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47 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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48 # safe and largely automated installation in a production Galaxy.
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49
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50 # If you opt for an HTML output, you get all the script outputs arranged
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51 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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52 # Ugly but really inexpensive.
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53 #
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54 # Patches appreciated please.
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55 #
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56 #
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57 # long route to June 2012 product
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58 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
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59 # derived from an integrated script model
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60 # called rgBaseScriptWrapper.py
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61 # Note to the unwary:
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62 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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63 # There is nothing stopping a malicious user doing whatever they choose
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64 # Extremely dangerous!!
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65 # Totally insecure. So, trusted users only
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66 #
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67 # preferred model is a developer using their throw away workstation instance - ie a private site.
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68 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
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69 #
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70
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71 import sys
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72 import shutil
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73 import subprocess
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74 import os
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75 import time
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76 import tempfile
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77 import optparse
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78 import tarfile
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79 import re
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80 import shutil
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81 import math
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82
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83 progname = os.path.split(sys.argv[0])[1]
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84 myversion = 'V000.2 June 2012'
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85 verbose = False
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86 debug = False
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87 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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88
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89 def timenow():
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90 """return current time as a string
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91 """
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92 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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93
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94 html_escape_table = {
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95 "&": "&amp;",
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96 ">": "&gt;",
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97 "<": "&lt;",
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98 "$": "\$"
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99 }
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100
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101 def html_escape(text):
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102 """Produce entities within text."""
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103 return "".join(html_escape_table.get(c,c) for c in text)
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104
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105 def cmd_exists(cmd):
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106 return subprocess.call("type " + cmd, shell=True,
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107 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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108
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109
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110 class ScriptRunner:
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111 """class is a wrapper for an arbitrary script
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112 """
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113
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114 def __init__(self,opts=None,treatbashSpecial=True):
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115 """
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116 cleanup inputs, setup some outputs
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117
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118 """
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119 self.useGM = cmd_exists('gm')
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120 self.useIM = cmd_exists('convert')
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121 self.useGS = cmd_exists('gs')
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122 self.temp_warned = False # we want only one warning if $TMP not set
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123 self.treatbashSpecial = treatbashSpecial
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124 if opts.output_dir: # simplify for the tool tarball
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125 os.chdir(opts.output_dir)
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126 self.thumbformat = 'png'
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127 self.opts = opts
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128 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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129 self.toolid = self.toolname
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130 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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131 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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132 self.xmlfile = '%s.xml' % self.toolname
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133 s = open(self.opts.script_path,'r').readlines()
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134 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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135 self.script = '\n'.join(s)
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136 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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137 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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138 tscript.write(self.script)
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139 tscript.close()
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140 self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
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141 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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142 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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143 if opts.output_dir: # may not want these complexities
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144 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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145 art = '%s.%s' % (self.toolname,opts.interpreter)
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146 artpath = os.path.join(self.opts.output_dir,art) # need full path
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147 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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148 artifact.write(self.script)
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149 artifact.close()
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150 self.cl = []
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151 self.html = []
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152 a = self.cl.append
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153 a(opts.interpreter)
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154 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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155 a(self.sfile)
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156 else:
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157 a('-') # stdin
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158 a(opts.input_tab)
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159 a(opts.output_tab)
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160 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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161 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
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162 self.test1Input = '%s_test1_input.xls' % self.toolname
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163 self.test1Output = '%s_test1_output.xls' % self.toolname
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164 self.test1HTML = '%s_test1_output.html' % self.toolname
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165
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166 def makeXML(self):
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167 """
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168 Create a Galaxy xml tool wrapper for the new script as a string to write out
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169 fixme - use templating or something less fugly than this example of what we produce
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170
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171 <tool id="reverse" name="reverse" version="0.01">
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172 <description>a tabular file</description>
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173 <command interpreter="python">
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174 reverse.py --script_path "$runMe" --interpreter "python"
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175 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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176 </command>
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177 <inputs>
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178 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
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179
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180 </inputs>
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181 <outputs>
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182 <data format="tabular" name="tab_file" label="${job_name}"/>
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183
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184 </outputs>
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185 <help>
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186
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187 **What it Does**
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188
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189 Reverse the columns in a tabular file
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190
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191 </help>
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192 <configfiles>
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193 <configfile name="runMe">
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194
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195 # reverse order of columns in a tabular file
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196 import sys
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197 inp = sys.argv[1]
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198 outp = sys.argv[2]
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199 i = open(inp,'r')
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200 o = open(outp,'w')
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201 for row in i:
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202 rs = row.rstrip().split('\t')
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203 rs.reverse()
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204 o.write('\t'.join(rs))
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205 o.write('\n')
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206 i.close()
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207 o.close()
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208
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209
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210 </configfile>
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211 </configfiles>
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212 </tool>
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213
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214 """
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215 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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216 %(tooldesc)s
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217 %(command)s
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218 <inputs>
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219 %(inputs)s
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220 </inputs>
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221 <outputs>
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222 %(outputs)s
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223 </outputs>
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224 <configfiles>
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225 <configfile name="runMe">
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226 %(script)s
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227 </configfile>
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228 </configfiles>
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229 %(tooltests)s
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230 <help>
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231 %(help)s
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232 </help>
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233 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
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234
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235 newCommand="""<command interpreter="python">
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236 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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237 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
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238 </command>""" # may NOT be an input or htmlout
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239 tooltestsTabOnly = """<tests><test>
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240 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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241 <param name="job_name" value="test1"/>
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242 <param name="runMe" value="$runMe"/>
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243 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
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244 </test></tests>"""
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245 tooltestsHTMLOnly = """<tests><test>
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246 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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247 <param name="job_name" value="test1"/>
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248 <param name="runMe" value="$runMe"/>
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249 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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250 </test></tests>"""
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251 tooltestsBoth = """<tests><test>
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252 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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253 <param name="job_name" value="test1"/>
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254 <param name="runMe" value="$runMe"/>
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255 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
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256 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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257 </test></tests>"""
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258 xdict = {}
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259 xdict['tool_version'] = self.opts.tool_version
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260 xdict['test1Input'] = self.test1Input
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261 xdict['test1HTML'] = self.test1HTML
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262 xdict['test1Output'] = self.test1Output
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263 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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264 xdict['tooltests'] = tooltestsBoth % xdict
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265 elif self.opts.make_HTML:
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266 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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267 else:
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268 xdict['tooltests'] = tooltestsTabOnly % xdict
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269 xdict['script'] = self.escapedScript
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270 # configfile is least painful way to embed script to avoid external dependencies
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271 # but requires escaping of <, > and $ to avoid Mako parsing
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272 if self.opts.help_text:
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273 xdict['help'] = open(self.opts.help_text,'r').read()
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274 else:
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275 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
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276 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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277 coda.append(self.indentedScript)
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278 coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
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279 coda.append('See %s for details of that project' % (toolFactoryURL))
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280 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
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281 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
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282 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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283 if self.opts.tool_desc:
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284 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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285 else:
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286 xdict['tooldesc'] = ''
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287 xdict['command_outputs'] = ''
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288 xdict['outputs'] = ''
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289 if self.opts.input_tab <> 'None':
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290 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
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291 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
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292 else:
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293 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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294 xdict['inputs'] = ''
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295 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
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296 xdict['toolname'] = self.toolname
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297 xdict['toolid'] = self.toolid
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298 xdict['interpreter'] = self.opts.interpreter
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299 xdict['scriptname'] = self.sfile
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300 if self.opts.make_HTML:
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301 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
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302 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
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303 if self.opts.output_tab <> 'None':
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304 xdict['command_outputs'] += ' --output_tab "$tab_file"'
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305 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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306 xdict['command'] = newCommand % xdict
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307 xmls = newXML % xdict
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308 xf = open(self.xmlfile,'w')
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309 xf.write(xmls)
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310 xf.write('\n')
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311 xf.close()
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312 # ready for the tarball
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313
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314
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315 def makeTooltar(self):
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316 """
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317 a tool is a gz tarball with eg
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318 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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319 """
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320 retval = self.run()
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321 if retval:
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322 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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323 sys.exit(1)
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324 self.makeXML()
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325 tdir = self.toolname
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326 os.mkdir(tdir)
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327 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
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328 testdir = os.path.join(tdir,'test-data')
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329 os.mkdir(testdir) # make tests directory
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330 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
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331 if self.opts.output_tab <> 'None':
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332 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
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333 if self.opts.make_HTML:
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334 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
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335 if self.opts.output_dir:
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336 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
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337 op = '%s.py' % self.toolname # new name
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338 outpiname = os.path.join(tdir,op) # path for the tool tarball
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339 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
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340 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
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341 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
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342 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
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343 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
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344 notes += pi
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345 outpi = open(outpiname,'w')
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346 outpi.write(''.join(notes))
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347 outpi.write('\n')
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348 outpi.close()
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349 stname = os.path.join(tdir,self.sfile)
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350 if not os.path.exists(stname):
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351 shutil.copyfile(self.sfile, stname)
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352 xtname = os.path.join(tdir,self.xmlfile)
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353 if not os.path.exists(xtname):
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354 shutil.copyfile(self.xmlfile,xtname)
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355 tarpath = "%s.gz" % self.toolname
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356 tar = tarfile.open(tarpath, "w:gz")
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357 tar.add(tdir,arcname=self.toolname)
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358 tar.close()
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359 shutil.copyfile(tarpath,self.opts.new_tool)
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360 shutil.rmtree(tdir)
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361 ## TODO: replace with optional direct upload to local toolshed?
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362 return retval
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363
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364
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365 def compressPDF(self,inpdf=None,thumbformat='png'):
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366 """need absolute path to pdf
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367 note that GS gets confoozled if no $TMP or $TEMP
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368 so we set it
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369 """
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370 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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371 our_env = os.environ.copy()
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372 if not (our_env.get('TMP',None) or our_env.get('TEMP',None)):
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373 our_env['TMP'] = '/tmp'
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374 if not self.temp_warned:
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375 print >> sys.stdout,'## WARNING - no $TMP or $TEMP!!! Please fix - using /tmp temporarily'
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376 self.temp_warned = True
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377 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
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378 sto = open(hlog,'w')
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379 outpdf = '%s_compressed' % inpdf
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380 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
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381 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
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382 retval1 = x.wait()
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383 sto.close()
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384 if retval1 == 0:
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385 os.unlink(inpdf)
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386 shutil.move(outpdf,inpdf)
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387 os.unlink(hlog)
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388 else:
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389 x = open(hlog,'r').readlines()
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diff changeset
390 print >> sys.stdout,x
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
391 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
392 sto = open(hlog,'w')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
393 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
394 if self.useGM:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
395 cl2 = ['gm', 'convert', inpdf, outpng]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
396 else: # assume imagemagick
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
397 cl2 = ['convert', inpdf, outpng]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
398 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
399 retval2 = x.wait()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
400 sto.close()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
401 if retval2 <> 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
402 x = open(hlog,'r').readlines()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
403 print >> sys.stdout,x
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
404 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
405 os.unlink(hlog)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
406 retval = retval1 or retval2
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
407 return retval
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
408
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
409
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
410 def getfSize(self,fpath,outpath):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
411 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
412 format a nice file size string
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
413 """
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fubar
parents:
diff changeset
414 size = ''
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
415 fp = os.path.join(outpath,fpath)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
416 if os.path.isfile(fp):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
417 size = '0 B'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
418 n = float(os.path.getsize(fp))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
419 if n > 2**20:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
420 size = '%1.1f MB' % (n/2**20)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
421 elif n > 2**10:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
422 size = '%1.1f KB' % (n/2**10)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
423 elif n > 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
424 size = '%d B' % (int(n))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
425 return size
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
426
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
427 def makeHtml(self):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
428 """ Create an HTML file content to list all the artifacts found in the output_dir
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
429 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
430
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
431 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
432 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
433 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
434 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
435 <title></title>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
436 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
437 </head>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
438 <body>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
439 <div class="toolFormBody">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
440 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
441 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
442 galhtmlpostfix = """</div></body></html>\n"""
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
443
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
444 flist = os.listdir(self.opts.output_dir)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
445 flist = [x for x in flist if x <> 'Rplots.pdf']
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
446 flist.sort()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
447 html = []
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
448 html.append(galhtmlprefix % progname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
449 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
450 fhtml = []
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
451 if len(flist) > 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
452 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
453 logfiles.sort()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
454 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
455 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
456 pdflist = []
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
457 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
458 for rownum,fname in enumerate(flist):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
459 dname,e = os.path.splitext(fname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
460 sfsize = self.getfSize(fname,self.opts.output_dir)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
461 if e.lower() == '.pdf' : # compress and make a thumbnail
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
462 thumb = '%s.%s' % (dname,self.thumbformat)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
463 pdff = os.path.join(self.opts.output_dir,fname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
464 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
465 if retval == 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
466 pdflist.append((fname,thumb))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
467 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
468 pdflist.append((fname,fname))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
469 if (rownum+1) % 2 == 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
470 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
471 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
472 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
473 for logfname in logfiles: # expect at least tlog - if more
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
474 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
475 sectionname = 'All tool run'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
476 if (len(logfiles) > 1):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
477 sectionname = 'Other'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
478 ourpdfs = pdflist
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
479 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
480 realname = os.path.basename(logfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
481 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
482 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
483 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
484 nacross = 1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
485 npdf = len(ourpdfs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
486
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
487 if npdf > 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
488 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
489 if int(nacross)**2 != npdf:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
490 nacross += 1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
491 nacross = int(nacross)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
492 width = min(400,int(1200/nacross))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
493 html.append('<H2>%s images and outputs</H2>' % sectionname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
494 html.append('<div class="toolFormTitle">Click on a thumbnail image to download the corresponding original PDF image</div>')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
495 ntogo = nacross # counter for table row padding with empty cells
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
496 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
497 for i,paths in enumerate(ourpdfs):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
498 fname,thumb = paths
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
499 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
500 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
501 if ((i+1) % nacross == 0):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
502 s += '</tr>\n'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
503 ntogo = 0
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
504 if i < (npdf - 1): # more to come
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
505 s += '<tr>'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
506 ntogo = nacross
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
507 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
508 ntogo -= 1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
509 html.append(s)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
510 if html[-1].strip().endswith('</tr>'):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
511 html.append('</table></div>\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
512 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
513 if ntogo > 0: # pad
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
514 html.append('<td>&nbsp;</td>'*ntogo)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
515 html.append('</tr></table></div>\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
516 logt = open(logfname,'r').readlines()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
517 logtext = [x for x in logt if x.strip() > '']
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
518 html.append('<H2>%s log output</H2>' % sectionname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
519 if len(logtext) > 1:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
520 html.append('\n<pre>\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
521 html += logtext
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
522 html.append('\n</pre>\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
523 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
524 html.append('%s is empty<br/>' % logfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
525 if len(fhtml) > 0:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
526 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
527 fhtml.append('</table></div><br/>')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
528 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
529 html += fhtml # add all non-pdf files to the end of the display
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
530 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
531 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
532 html.append(galhtmlpostfix)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
533 htmlf = file(self.opts.output_html,'w')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
534 htmlf.write('\n'.join(html))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
535 htmlf.write('\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
536 htmlf.close()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
537 self.html = html
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
538
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
539
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
540 def run(self):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
541 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
542 scripts must be small enough not to fill the pipe!
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
543 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
544 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
545 retval = self.runBash()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
546 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
547 if self.opts.output_dir:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
548 ste = open(self.elog,'w')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
549 sto = open(self.tlog,'w')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
550 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
551 sto.flush()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
552 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
553 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
554 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
555 p.stdin.write(self.script)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
556 p.stdin.close()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
557 retval = p.wait()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
558 if self.opts.output_dir:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
559 sto.close()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
560 ste.close()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
561 err = open(self.elog,'r').readlines()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
562 if retval <> 0 and err: # problem
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
563 print >> sys.stderr,err
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
564 if self.opts.make_HTML:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
565 self.makeHtml()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
566 return retval
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
567
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
568 def runBash(self):
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
569 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
570 cannot use - for bash so use self.sfile
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
571 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
572 if self.opts.output_dir:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
573 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
574 sto = open(self.tlog,'w')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
575 sto.write(s)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
576 sto.flush()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
577 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
578 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
579 p = subprocess.Popen(self.cl,shell=False)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
580 retval = p.wait()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
581 if self.opts.output_dir:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
582 sto.close()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
583 if self.opts.make_HTML:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
584 self.makeHtml()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
585 return retval
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
586
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
587
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
588 def main():
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
589 u = """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
590 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
591 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
592 </command>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
593 """
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
594 op = optparse.OptionParser()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
595 a = op.add_option
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
596 a('--script_path',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
597 a('--tool_name',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
598 a('--interpreter',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
599 a('--output_dir',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
600 a('--output_html',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
601 a('--input_tab',default="None")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
602 a('--output_tab',default="None")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
603 a('--user_email',default='Unknown')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
604 a('--bad_user',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
605 a('--make_Tool',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
606 a('--make_HTML',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
607 a('--help_text',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
608 a('--tool_desc',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
609 a('--new_tool',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
610 a('--tool_version',default=None)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
611 opts, args = op.parse_args()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
612 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
613 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
614 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
615 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
616 if opts.output_dir:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
617 try:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
618 os.makedirs(opts.output_dir)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
619 except:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
620 pass
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
621 r = ScriptRunner(opts)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
622 if opts.make_Tool:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
623 retcode = r.makeTooltar()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
624 else:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
625 retcode = r.run()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
626 os.unlink(r.sfile)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
627 if retcode:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
628 sys.exit(retcode) # indicate failure to job runner
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
629
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
630
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
631 if __name__ == "__main__":
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
632 main()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
633
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
634