| Previous changeset 17:903e3748f735 (2014-03-23) Next changeset 19:4bfe405f76ed (2014-03-23) |
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Commit message:
removed dependencies |
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modified:
rgToolFactory.py |
| b |
| diff -r 903e3748f735 -r a986c9f88d38 rgToolFactory.py --- a/rgToolFactory.py Sun Mar 23 07:12:47 2014 -0400 +++ b/rgToolFactory.py Sun Mar 23 07:28:32 2014 -0400 |
| b |
| @@ -8,6 +8,8 @@ # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home # # march 2014 +# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript +# grrrrr - night before a demo # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable # # added ghostscript and graphicsmagick as dependencies @@ -95,10 +97,10 @@ toolhtmldepskel = """<?xml version="1.0"?> <tool_dependency> <package name="ghostscript" version="9.10"> - <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" /> + <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" /> </package> <package name="graphicsmagick" version="1.3.18"> - <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" /> + <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" /> </package> <readme> %s @@ -362,11 +364,12 @@ hlp = open(self.opts.help_text,'r').read() else: hlp = 'Please ask the tool author for help as none was supplied at tool generation\n' - tooldepcontent = toolhtmldepskel % hlp - depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w') - depf.write(tooldepcontent) - depf.write('\n') - depf.close() + if self.opts.include_dependencies: + tooldepcontent = toolhtmldepskel % hlp + depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w') + depf.write(tooldepcontent) + depf.write('\n') + depf.close() if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. testdir = os.path.join(tdir,'test-data') os.mkdir(testdir) # make tests directory @@ -653,6 +656,7 @@ a('--tool_desc',default=None) a('--new_tool',default=None) a('--tool_version',default=None) + a('--include_dependencies',default=None) opts, args = op.parse_args() 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) assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' |