Hi galaxy developers, Just want to double-check, there is no way to import some kind of galaxy tool context info into python code you are running for a tool?
best, leandro On Fri, Apr 15, 2011 at 8:03 PM, Leandro Hermida <soft...@leandrohermida.com > wrote: > On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > >> On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida >> <soft...@leandrohermida.com> wrote: >> > On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock <p.j.a.c...@googlemail.com> >> > wrote: >> >> >> >> For standard Python tools in Galaxy, I'm using >> >> os.path.split(sys.argv[0])[0] >> >> to get the path, which on reflection probably should be written as >> >> os.path.dirname(sys.argv[0]) as you suggest. >> >> >> >> What do __file__ and sys.argv[0] give you? The simplest way to debug >> >> this is to add a print statement, since Galaxy will show the stdout. >> >> >> > >> > Hi Peter, >> > >> > __file__ throws an error: global name '__file__' is not defined >> >> I guess the script is being loaded as a string, and run with eval(...) >> or something like that. It would also explain why sys.argv[0] would >> be one of the Galaxy script files. >> >> > os.path.abspath(os.path.dirname(sys.argv[0])) gives me >> > /path/to/galaxy/scripts directory which is two levels up from what the >> tool >> > directory I want for example /path/to/galaxy/tools/mytool >> >> So combine that with ../tools/mytool/ and you're done? OK, you have >> to know the name of the folder your tool *should* be in... so not a >> perfect solution. > > > Thanks Peter, yes that's the same idea I did as a quick fix.... also don't > like the fact that my tool directory is hard-coded but oh well. There must > be a way within Python in Galaxy importing something from Galaxy that has > the current tool directory path, it would seem that Galaxy needs to know > this and would store it anyway? > > best, > Leandro > >
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