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annotate fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.py @ 2:b55b59435fb1 draft

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Now with bash working I think. Special case but working..
author fubar
date Mon, 13 Aug 2012 06:27:26 -0400
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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 11 2012
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11 # changed to use shell=False and cl as a sequence
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12
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13 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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14 # It also serves as the wrapper for the new tool.
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15 #
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16 # you paste and run your script
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17 # Only works for simple scripts that read one input from the history.
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18 # Optionally can write one new history dataset,
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19 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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20
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21 # DO NOT install on a public or important site - please.
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22
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23 # installed generated tools are fine if the script is safe.
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24 # They just run normally and their user cannot do anything unusually insecure
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25 # but please, practice safe toolshed.
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26 # Read the fucking code before you install any tool
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27 # especially this one
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28
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29 # After you get the script working on some test data, you can
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30 # optionally generate a toolshed compatible gzip file
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31 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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32 # safe and largely automated installation in a production Galaxy.
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33
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34 # If you opt for an HTML output, you get all the script outputs arranged
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35 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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36 # Ugly but really inexpensive.
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37 #
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38 # Patches appreciated please.
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39 #
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40 #
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41 # long route to June 2012 product
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42 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
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43 # derived from an integrated script model
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44 # called rgBaseScriptWrapper.py
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45 # Note to the unwary:
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46 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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47 # There is nothing stopping a malicious user doing whatever they choose
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48 # Extremely dangerous!!
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49 # Totally insecure. So, trusted users only
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50 #
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51 # preferred model is a developer using their throw away workstation instance - ie a private site.
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52 # 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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53 #
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54
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55 #
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56 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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57 #
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58 # all rights reserved
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59 # Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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60
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61 import sys
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62 import shutil
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63 import subprocess
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64 import os
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65 import time
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66 import tempfile
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67 import optparse
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68 import tarfile
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69 import re
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70 import shutil
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71 import math
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72
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73 progname = os.path.split(sys.argv[0])[1]
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74 myversion = 'V000.2 June 2012'
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75 verbose = False
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76 debug = False
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77 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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78
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79 def timenow():
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80 """return current time as a string
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81 """
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82 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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83
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84
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85 class ScriptRunner:
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86 """class is a wrapper for an arbitrary script
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87 """
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88
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89 def __init__(self,opts=None,treatbashSpecial=True):
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90 """
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91 cleanup inputs, setup some outputs
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92
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93 """
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94 self.treatbashSpecial = treatbashSpecial
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95 if opts.output_dir: # simplify for the tool tarball
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96 os.chdir(opts.output_dir)
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97 self.thumbformat = 'jpg'
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98 self.opts = opts
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99 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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100 self.toolid = self.toolname
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101 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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102 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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103 self.xmlfile = '%s.xml' % self.toolname
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104 s = open(self.opts.script_path,'r').readlines()
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105 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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106 self.script = '\n'.join(s)
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107 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=opts.interpreter)
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108 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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109 tscript.write(self.script)
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110 tscript.close()
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111 self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
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112 if opts.output_dir: # may not want these complexities
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113 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
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114 art = '%s.%s' % (self.toolname,opts.interpreter)
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115 artpath = os.path.join(self.opts.output_dir,art) # need full path
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116 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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117 artifact.write(self.script)
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118 artifact.close()
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119 self.cl = []
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120 self.html = []
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121 a = self.cl.append
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122 a(opts.interpreter)
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123 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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124 a(self.sfile)
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125 else:
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126 a('-') # stdin
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127 a(opts.input_tab)
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128 a(opts.output_tab)
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129 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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130 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
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131 self.test1Input = '%s_test1_input.xls' % self.toolname
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132 self.test1Output = '%s_test1_output.xls' % self.toolname
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133 self.test1HTML = '%s_test1_output.html' % self.toolname
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134
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135 def makeXML(self):
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136 """
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137 Create a Galaxy xml tool wrapper for the new script as a string to write out
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138 fixme - use templating or something less fugly than this example of what we produce
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139
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140 <tool id="reverse" name="reverse" version="0.01">
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141 <description>a tabular file</description>
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142 <command interpreter="python">
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143 reverse.py --script_path "$runMe" --interpreter "python"
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144 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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145 </command>
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146 <inputs>
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147 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
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148
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149 </inputs>
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150 <outputs>
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151 <data format="tabular" name="tab_file" label="${job_name}"/>
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152
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153 </outputs>
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154 <help>
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155
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156 **What it Does**
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157
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158 Reverse the columns in a tabular file
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159
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160 </help>
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161 <configfiles>
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162 <configfile name="runMe">
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163
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164 # reverse order of columns in a tabular file
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165 import sys
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166 inp = sys.argv[1]
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167 outp = sys.argv[2]
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168 i = open(inp,'r')
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169 o = open(outp,'w')
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fubar
parents:
diff changeset
170 for row in i:
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fubar
parents:
diff changeset
171 rs = row.rstrip().split('\t')
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fubar
parents:
diff changeset
172 rs.reverse()
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fubar
parents:
diff changeset
173 o.write('\t'.join(rs))
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fubar
parents:
diff changeset
174 o.write('\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
175 i.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
176 o.close()
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fubar
parents:
diff changeset
177
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
178
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
179 </configfile>
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fubar
parents:
diff changeset
180 </configfiles>
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fubar
parents:
diff changeset
181 </tool>
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fubar
parents:
diff changeset
182
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
183 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
184 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
185 %(tooldesc)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
186 %(command)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
187 <inputs>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
188 %(inputs)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
189 </inputs>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
190 <outputs>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
191 %(outputs)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
192 </outputs>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
193 <configfiles>
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fubar
parents:
diff changeset
194 <configfile name="runMe">
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
195 %(script)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
196 </configfile>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
197 </configfiles>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
198 %(tooltests)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
199 <help>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
200 %(help)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
201 </help>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
202 </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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fubar
parents:
diff changeset
203
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
204 newCommand="""<command interpreter="python">
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
205 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
206 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
207 </command>""" # may NOT be an input or htmlout
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
208 tooltestsTabOnly = """<tests><test>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
209 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
210 <param name="job_name" value="test1"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
211 <param name="runMe" value="$runMe"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
212 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
213 </test></tests>"""
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
214 tooltestsHTMLOnly = """<tests><test>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
215 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
216 <param name="job_name" value="test1"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
217 <param name="runMe" value="$runMe"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
218 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
219 </test></tests>"""
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
220 tooltestsBoth = """<tests><test>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
221 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
222 <param name="job_name" value="test1"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
223 <param name="runMe" value="$runMe"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
224 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
225 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
226 </test></tests>"""
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
227 xdict = {}
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
228 xdict['tool_version'] = self.opts.tool_version
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fubar
parents:
diff changeset
229 xdict['test1Input'] = self.test1Input
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
230 xdict['test1HTML'] = self.test1HTML
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
231 xdict['test1Output'] = self.test1Output
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
232 if self.opts.make_HTML and self.opts.output_tab <> 'None':
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
233 xdict['tooltests'] = tooltestsBoth % xdict
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
234 elif self.opts.make_HTML:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
235 xdict['tooltests'] = tooltestsHTMLOnly % xdict
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
236 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
237 xdict['tooltests'] = tooltestsTabOnly % xdict
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
238 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
239 if self.opts.help_text:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
240 xdict['help'] = open(self.opts.help_text,'r').read()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
241 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
242 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
243 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
244 coda.append(self.indentedScript)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
245 coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
246 coda.append('See %s for details of that project' % (toolFactoryURL))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
247 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
248 if self.opts.tool_desc:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
249 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
250 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
251 xdict['tooldesc'] = ''
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
252 xdict['command_outputs'] = ''
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
253 xdict['outputs'] = ''
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
254 if self.opts.input_tab <> 'None':
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
255 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
256 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
257 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
258 xdict['command_inputs'] = '' # assume no input - eg a random data generator
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
259 xdict['inputs'] = ''
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
260 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
261 xdict['toolname'] = self.toolname
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
262 xdict['toolid'] = self.toolid
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
263 xdict['interpreter'] = self.opts.interpreter
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
264 xdict['scriptname'] = self.sfile
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
265 if self.opts.make_HTML:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
266 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
267 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
268 if self.opts.output_tab <> 'None':
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
269 xdict['command_outputs'] += ' --output_tab "$tab_file"'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
270 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
271 xdict['command'] = newCommand % xdict
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
272 xmls = newXML % xdict
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
273 xf = open(self.xmlfile,'w')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
274 xf.write(xmls)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
275 xf.write('\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
276 xf.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
277 # ready for the tarball
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
278
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
279
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
280 def makeTooltar(self):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
281 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
282 a tool is a gz tarball with eg
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
283 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
284 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
285 retval = self.run()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
286 if retval:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
287 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
288 sys.exit(1)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
289 self.makeXML()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
290 tdir = self.toolname
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
291 os.mkdir(tdir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
292 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
293 testdir = os.path.join(tdir,'test-data')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
294 os.mkdir(testdir) # make tests directory
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
295 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
296 if self.opts.output_tab <> 'None':
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
297 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
298 if self.opts.make_HTML:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
299 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
300 if self.opts.output_dir:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
301 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
302 op = '%s.py' % self.toolname # new name
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
303 outpiname = os.path.join(tdir,op) # path for the tool tarball
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
304 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
305 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
306 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
307 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
308 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
309 notes += pi
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
310 outpi = open(outpiname,'w')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
311 outpi.write(''.join(notes))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
312 outpi.write('\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
313 outpi.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
314 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
315 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
316 tarpath = "%s.gz" % self.toolname
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
317 tar = tarfile.open(tarpath, "w:gz")
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
318 tar.add(tdir,arcname=self.toolname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
319 tar.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
320 shutil.copyfile(tarpath,self.opts.new_tool)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
321 shutil.rmtree(tdir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
322 ## TODO: replace with optional direct upload to local toolshed?
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
323 return retval
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
324
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
325 def compressPDF(self,inpdf=None,thumbformat='png'):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
326 """need absolute path to pdf
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
327 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
328 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
329 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
330 sto = open(hlog,'w')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
331 outpdf = '%s_compressed' % inpdf
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
332 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
333 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
334 retval1 = x.wait()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
335 if retval1 == 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
336 os.unlink(inpdf)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
337 shutil.move(outpdf,inpdf)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
338 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
339 cl2 = ['convert', inpdf, outpng]
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
340 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
341 retval2 = x.wait()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
342 sto.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
343 retval = retval1 or retval2
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
344 return retval
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
345
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
346
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
347 def getfSize(self,fpath,outpath):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
348 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
349 format a nice file size string
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
350 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
351 size = ''
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
352 fp = os.path.join(outpath,fpath)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
353 if os.path.isfile(fp):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
354 size = '0 B'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
355 n = float(os.path.getsize(fp))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
356 if n > 2**20:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
357 size = '%1.1f MB' % (n/2**20)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
358 elif n > 2**10:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
359 size = '%1.1f KB)' % (n/2**10)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
360 elif n > 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
361 size = '%d B' % (int(n))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
362 return size
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
363
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
364 def makeHtml(self):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
365 """ Create an HTML file content to list all the artifacts found in the output_dir
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
366 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
367
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
368 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
369 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
370 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
371 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
372 <title></title>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
373 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
374 </head>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
375 <body>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
376 <div class="toolFormBody">
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
377 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
378 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/>"""
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
379 galhtmlpostfix = """</div></body></html>\n"""
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
380
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
381 flist = os.listdir(self.opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
382 flist = [x for x in flist if x <> 'Rplots.pdf']
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
383 flist.sort()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
384 html = []
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
385 html.append(galhtmlprefix % progname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
386 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
387 fhtml = []
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
388 if len(flist) > 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
389 pdflist = []
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
390 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
391 nacross = 1
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
392 if npdf > 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
393 nacross = int(round(math.log(npdf,2)))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
394 nacross = max(1,nacross)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
395 width = min(400,int(1200/nacross))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
396 for rownum,fname in enumerate(flist):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
397 dname,e = os.path.splitext(fname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
398 sfsize = self.getfSize(fname,self.opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
399 if e.lower() == '.pdf' : # compress and make a thumbnail
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
400 thumb = '%s.%s' % (dname,self.thumbformat)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
401 pdff = os.path.join(self.opts.output_dir,fname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
402 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
403 if retval == 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
404 pdflist.append((fname,thumb))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
405 if (rownum+1) % 2 == 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
406 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
407 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
408 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
409 ntogo = nacross # counter for table row padding with empty cells
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
410 if len(pdflist) > 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
411 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
412 for i,paths in enumerate(pdflist):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
413 fname,thumb = paths
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
414 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
415 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
416 if ((i+1) % nacross == 0):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
417 s += '</tr>\n'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
418 ntogo = 0
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
419 if i < (npdf - 1): # more to come
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
420 s += '<tr>'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
421 ntogo = nacross
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
422 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
423 ntogo -= 1
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
424 html.append(s)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
425 if html[-1].strip().endswith('</tr>'):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
426 html.append('</table></div>\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
427 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
428 if ntogo > 0: # pad
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
429 html.append('<td>&nbsp;</td>'*ntogo)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
430 html.append('</tr></table></div>\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
431 if len(fhtml) > 0:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
432 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')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
433 fhtml.append('</table></div><br/>')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
434 html += fhtml # add all non-pdf files to the end of the display
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
435 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
436 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
437 rlog = open(self.tlog,'r').readlines()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
438 rlog = [x for x in rlog if x.strip() > '']
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
439 if len(rlog) > 1:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
440 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
441 html += rlog
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
442 html.append('</pre>\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
443 html.append(galhtmlattr % (self.toolname))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
444 html.append(galhtmlpostfix)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
445 htmlf = file(self.opts.output_html,'w')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
446 htmlf.write('\n'.join(html))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
447 htmlf.write('\n')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
448 htmlf.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
449 self.html = html
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
450
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
451
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
452 def run(self):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
453 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
454 scripts must be small enough not to fill the pipe!
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
455 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
456 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
457 retval = self.runBash()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
458 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
459 if self.opts.output_dir:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
460 sto = open(self.tlog,'w')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
461 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
462 sto.flush()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
463 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
464 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
465 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
466 p.stdin.write(self.script)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
467 p.stdin.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
468 retval = p.wait()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
469 if self.opts.output_dir:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
470 sto.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
471 if self.opts.make_HTML:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
472 self.makeHtml()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
473 os.unlink(self.sfile)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
474 return retval
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
475
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
476 def runBash(self):
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
477 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
478 cannot use - for bash so use self.sfile
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
479 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
480 if self.opts.output_dir:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
481 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
482 sto = open(self.tlog,'w')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
483 sto.write(s)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
484 sto.flush()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
485 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
486 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
487 p = subprocess.Popen(self.cl,shell=False)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
488 retval = p.wait()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
489 if self.opts.output_dir:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
490 sto.close()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
491 if self.opts.make_HTML:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
492 self.makeHtml()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
493 return retval
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
494
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
495
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
496 def main():
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
497 u = """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
498 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
499 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
500 </command>
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
501 """
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
502 op = optparse.OptionParser()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
503 a = op.add_option
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
504 a('--script_path',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
505 a('--tool_name',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
506 a('--interpreter',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
507 a('--output_dir',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
508 a('--output_html',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
509 a('--input_tab',default="None")
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
510 a('--output_tab',default="None")
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
511 a('--user_email',default='Unknown')
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
512 a('--bad_user',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
513 a('--make_Tool',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
514 a('--make_HTML',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
515 a('--help_text',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
516 a('--tool_desc',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
517 a('--new_tool',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
518 a('--tool_version',default=None)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
519 opts, args = op.parse_args()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
520 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)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
521 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
522 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
523 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
524 if opts.output_dir:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
525 try:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
526 os.makedirs(opts.output_dir)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
527 except:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
528 pass
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
529 r = ScriptRunner(opts)
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
530 if opts.make_Tool:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
531 retcode = r.makeTooltar()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
532 else:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
533 retcode = r.run()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
534 if retcode:
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
535 sys.exit(retcode) # indicate failure to job runner
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
536
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
537
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
538 if __name__ == "__main__":
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
539 main()
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
540
b55b59435fb1 Now with bash working I think. Special case but working..
fubar
parents:
diff changeset
541