Mercurial > repos > fubar > toolfactory
changeset 11:704ccaade924 draft
Uploaded
author | fubar |
---|---|
date | Thu, 20 Mar 2014 05:50:38 -0400 |
parents | 59bce2efadfe |
children | a898ba82496e |
files | rgToolFactory.py |
diffstat | 1 files changed, 30 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/rgToolFactory.py Thu Mar 20 05:03:17 2014 -0400 +++ b/rgToolFactory.py Thu Mar 20 05:50:38 2014 -0400 @@ -8,6 +8,8 @@ # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home # # march 2014 +# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable +# # added ghostscript and graphicsmagick as dependencies # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp # errors ensued @@ -88,6 +90,21 @@ debug = False toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' +# if we do html we need these dependencies +toolhtmldep = """<?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/" /> + </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/" /> + </package> + <readme> + %s + </readme> +</tool_dependency> +""" + def timenow(): """return current time as a string """ @@ -130,7 +147,7 @@ self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. self.toolid = self.toolname self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later - self.pyfile = self.myname # crude but efficient - the cruft won't hurt much + self.pyfile = self.myname # crude but efficient - the cruft won't hurt muchself.tooldepfile) self.xmlfile = '%s.xml' % self.toolname s = open(self.opts.script_path,'r').readlines() s = [x.rstrip() for x in s] # remove pesky dos line endings if needed @@ -233,7 +250,7 @@ %(help)s </help> </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto - + newCommand="""<command interpreter="python"> %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s @@ -323,9 +340,19 @@ if retval: print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' sys.exit(1) - self.makeXML() tdir = self.toolname os.mkdir(tdir) + self.makeXML() + if self.opts.make_HTML: + if self.opts.help_text: + 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' + tooldeps = toolhtmldep % hlp + depf = open('tool_dependencies.xml','w') + depf.write(hlp) + 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