| Previous changeset 13:00777b83aaca (2015-01-15) Next changeset 15:dd6cf2ddaac7 (2015-01-28) |
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Commit message:
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modified:
rgToolFactory2.py |
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| diff -r 00777b83aaca -r 3635f4518c4d rgToolFactory2.py --- a/rgToolFactory2.py Thu Jan 15 07:43:13 2015 -0500 +++ b/rgToolFactory2.py Tue Jan 20 19:03:18 2015 -0500 |
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| @@ -10,7 +10,9 @@ # January 2015 # in the process of building a complex tool # added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package -# need to add that package to tool_dependencies +# add that package to tool_dependencies +# Note that once the generated tool is loaded, it will have that package's env.sh loaded automagically so there is no +# --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path. # # sept 2014 added additional params from # https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default @@ -194,6 +196,7 @@ <readme> %(readme)s + This file was autogenerated by the Galaxy Tool Factory 2 </readme> </tool_dependency> """ @@ -208,6 +211,7 @@ </package> <readme> %(readme)s + This file was autogenerated by the Galaxy Tool Factory 2 </readme> </tool_dependency> """ @@ -216,6 +220,7 @@ <tool_dependency> <readme> %(readme)s + This file was autogenerated by the Galaxy Tool Factory 2 </readme> </tool_dependency> """ @@ -295,6 +300,8 @@ %(help)s +This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2 +https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2 </help> <citations> %(citations)s @@ -427,14 +434,14 @@ self.interp_revision = None self.interp_version = None if opts.envshpath <> 'system': # need to parse out details for our tool_dependency - try: + try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play + packdetails = opts.envshpath.split(os.path.sep)[-4:-1] # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c'] self.interpreter_owner = packdetails[0] self.interpreter_pack = packdetails[1] self.interpreter_name = packdetails[1].split('_')[1].upper() self.interpreter_revision = packdetails[2] - self.interpreter_version = '.'.join(self.interpreter_pack.split('_')[2:]) - # hope our naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play + self.interpreter_version = '.'.join(packdetails[1].split('_')[2:]) except: pass self.outFormats = opts.output_format @@ -617,7 +624,7 @@ else: hlp = 'Please ask the tool author for help as none was supplied at tool generation\n' readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name, - 'interpreter_owner':self.interpreter_owner} + 'interpreter_owner':self.interpreter_owner,'interpreter_pack':self.interpreter_pack} if self.opts.include_dependencies == "yes": if self.opts.envshpath == 'system': tooldepcontent = self.toolhtmldepskel % readme_dict @@ -629,23 +636,22 @@ depf.write(tooldepcontent) depf.write('\n') depf.close() - if self.opts.input_tab: # no reproducible test otherwise? TODO: maybe.. - testdir = os.path.join(tdir,'test-data') - os.mkdir(testdir) # make tests directory - for i,intab in enumerate(self.opts.input_tab): - si = self.opts.input_tab[i] - if si.find(',') <> -1: - s = si.split(',')[0] - si = s - dest = os.path.join(testdir,os.path.basename(si)) - if si <> dest: - shutil.copyfile(si,dest) - if self.opts.output_tab: - shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) - if self.opts.make_HTML: - shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) - if self.opts.output_dir: - shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) + testdir = os.path.join(tdir,'test-data') + os.mkdir(testdir) # make tests directory + for i,intab in enumerate(self.opts.input_tab): + si = self.opts.input_tab[i] + if si.find(',') <> -1: + s = si.split(',')[0] + si = s + dest = os.path.join(testdir,os.path.basename(si)) + if si <> dest: + shutil.copyfile(si,dest) + if self.opts.output_tab: + shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) + if self.opts.make_HTML: + shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) + if self.opts.output_dir: + shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) outpif = '%s.py' % self.toolname # new name outpiname = os.path.join(tdir,outpif) # path for the tool tarball pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) |